Datasets:
gabrielaltay
/
archs4-human-gene-v2.5-meta-sample

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1
sample: GM11993,family: 1362,relation: paternal grandmother,protocol: non-directional
210 washtenaw ave
Ann Arbor
USA
HHMI/University of Michigan
Isabel,Xiaorong,Wang
Low-quality bases as designated by CASAVA (v1.8) were trimmed from the 3' end of reads.,Reads were aligned using GSNAP (v2012-04-10). (Read length + 2)/12 – 2 or fewer mismatches were tolerated. Alignments to novel exon-exon junctions and known junctions as defined by RefSeq (downloaded March 7, 2011) and Gencode (v3c) were allowed. A list of SNPs in the CEU population from Hapmap (release #28) and 1000 Genomes (pilot project) was used to allow for SNP-tolerant alignments.,Variants were called with Samtools (v0.1.16),Genome_build: hg18
RNA-seq libraries were prepared following Illumina's recommendations. Briefly, cells were harvested 24 hours after addition of fresh medium, and total RNA was extracted using the RNeasy Mini kit with DNase treatment (Qiagen). Poly-A mRNA was isolated and fragmented. First strand cDNA was prepared using reverse transcriptase and random hexamers. After second strand cDNA synthesis, ends were repaired and a single ‘A’ base was added followed by adapter sequences. Library fragments were selected for an average size of 200 to 260 base pairs, PCR amplified, and then sequenced using Illumina next-generation sequencing technology.
GSM957430
Illumina HiSeq 2000
May 15 2019
cDNA
transcriptomic
RNA-Seq
total RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX158884,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01086646
GSM957430
GSE39167
0.003275
cultured B-cells
Public on Jul 01 2017
Jul 06 2012
9606
Family1362Set_GM11993
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX158884
https://www.ncbi.nlm.nih.gov/biosample/SAMN01086646
1
sample: GM11994,family: 1362,relation: maternal grandfather,protocol: non-directional
210 washtenaw ave
Ann Arbor
USA
HHMI/University of Michigan
Isabel,Xiaorong,Wang
Low-quality bases as designated by CASAVA (v1.8) were trimmed from the 3' end of reads.,Reads were aligned using GSNAP (v2012-04-10). (Read length + 2)/12 – 2 or fewer mismatches were tolerated. Alignments to novel exon-exon junctions and known junctions as defined by RefSeq (downloaded March 7, 2011) and Gencode (v3c) were allowed. A list of SNPs in the CEU population from Hapmap (release #28) and 1000 Genomes (pilot project) was used to allow for SNP-tolerant alignments.,Variants were called with Samtools (v0.1.16),Genome_build: hg18
RNA-seq libraries were prepared following Illumina's recommendations. Briefly, cells were harvested 24 hours after addition of fresh medium, and total RNA was extracted using the RNeasy Mini kit with DNase treatment (Qiagen). Poly-A mRNA was isolated and fragmented. First strand cDNA was prepared using reverse transcriptase and random hexamers. After second strand cDNA synthesis, ends were repaired and a single ‘A’ base was added followed by adapter sequences. Library fragments were selected for an average size of 200 to 260 base pairs, PCR amplified, and then sequenced using Illumina next-generation sequencing technology.
GSM957431
Illumina HiSeq 2000
May 15 2019
cDNA
transcriptomic
RNA-Seq
total RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX158885,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01086647
GSM957431
GSE39167
0.002758
cultured B-cells
Public on Jul 01 2017
Jul 06 2012
9606
Family1362Set_GM11994
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX158885
https://www.ncbi.nlm.nih.gov/biosample/SAMN01086647
1
sample: GM11996,family: 1362,relation: son,protocol: non-directional
210 washtenaw ave
Ann Arbor
USA
HHMI/University of Michigan
Isabel,Xiaorong,Wang
Low-quality bases as designated by CASAVA (v1.8) were trimmed from the 3' end of reads.,Reads were aligned using GSNAP (v2012-04-10). (Read length + 2)/12 – 2 or fewer mismatches were tolerated. Alignments to novel exon-exon junctions and known junctions as defined by RefSeq (downloaded March 7, 2011) and Gencode (v3c) were allowed. A list of SNPs in the CEU population from Hapmap (release #28) and 1000 Genomes (pilot project) was used to allow for SNP-tolerant alignments.,Variants were called with Samtools (v0.1.16),Genome_build: hg18
RNA-seq libraries were prepared following Illumina's recommendations. Briefly, cells were harvested 24 hours after addition of fresh medium, and total RNA was extracted using the RNeasy Mini kit with DNase treatment (Qiagen). Poly-A mRNA was isolated and fragmented. First strand cDNA was prepared using reverse transcriptase and random hexamers. After second strand cDNA synthesis, ends were repaired and a single ‘A’ base was added followed by adapter sequences. Library fragments were selected for an average size of 200 to 260 base pairs, PCR amplified, and then sequenced using Illumina next-generation sequencing technology.
GSM957433
Illumina HiSeq 2000
May 15 2019
cDNA
transcriptomic
RNA-Seq
total RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX158887,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01086649
GSM957433
GSE39167
0.01966
cultured B-cells
Public on Jul 01 2017
Jul 06 2012
9606
Family1362Set_GM11996
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX158887
https://www.ncbi.nlm.nih.gov/biosample/SAMN01086649
1
cell type: HEK293T,cell source: ATCC CRL-11268™,tissue: Kidney,genotype: wild type
Meibergdreef 61
Amsterdam
Netherlands
UniQure
Piotr,,Maczuga
Illumina Casava1.8.2 software used for basecalling.,The raw sequencing data produced was processed removing the sequence reads which were of too low quality (only "passing filter" reads were selected), and discarding reads that aligned against the PhiX control. In total, we generated 16016701 reads for sample miApoB, and 15843150 reads for sample shApoB.,The obtained reads were adaptor-trimmed, which decreased the average read size from ~36bp to ~25bp. The custom adapter sequenced used for trimming all the bases extending 5’ was: GTGACTGGAGTTCC-TTGGCACCCGAGAATTCCA.,Next, both data sets from shApoB and miApoB samples were grouped based on the match to the reference sequence and the obtained unique small RNAs were aligned to the sequence of pre-miApoB: GATCCTGGAGGCTTGC-TGAAGGCTGTATGCTGATGGACAGGTCAATCAATCTTGTTTTGGCCACTGACTGACAAGATTGAGACCTGTCCATCAGGACACAAGGCCTGTTACTAGCACTCACATGGAACAAATGGCCCAGATCTGGCCGCAG or shApoB: GATCCCCGATTGATTGACCTGTCCATTTCAAGAGAATGGACAGGTCAATCAATC-TTTTTCAGCTT sequence, respectively.,Supplementary_files_format_and_content: Spreadsheet including reads abundancy. Figure 1 and showing alliingment with references miApoB and shApoB sequences,Genome_build: miRBase Release 18: November 2011
HEK293T cells were transfected with 4 µg shApoB- or miApoB-expression plasmids using Lipofectamine 2000 reagent using manufacturers protocol and total RNA was isolated from cells 48 hr post-transfection using Trizol. Small RNA sequencing libraries were generated using high-quality total RNA as input and the NEXTflex Small RNA Sequencing kit (Bioo Scientific, USA). Briefly, the small RNA species were subjected to ligation with 3' and 5' RNA adapters, first strand reverse transcription, and PCR amplification. Sample-specific barcodes were introduced in the PCR step. The PCR products were separated on TBE-PAGE electrophoresis and the expected band around 140-160bp was recovered for each sample. The libraries were multiplexed, clustered, and sequenced on an Illumina HiSeq 2000.
GSM957705
Illumina HiSeq 2000
May 15 2019
size fractionation
transcriptomic
RNA-Seq
total RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX158351,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01086231
GSM957705
GSE39187
0
shApoB
Public on Jul 10 2012
Jul 09 2012
9606
shApoB (small RNA)
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX158351
https://www.ncbi.nlm.nih.gov/biosample/SAMN01086231
1
cell type: HEK293T,cell source: ATCC CRL-11268™,tissue: Kidney,genotype: wild type
Meibergdreef 61
Amsterdam
Netherlands
UniQure
Piotr,,Maczuga
Illumina Casava1.8.2 software used for basecalling.,The raw sequencing data produced was processed removing the sequence reads which were of too low quality (only "passing filter" reads were selected), and discarding reads that aligned against the PhiX control. In total, we generated 16016701 reads for sample miApoB, and 15843150 reads for sample shApoB.,The obtained reads were adaptor-trimmed, which decreased the average read size from ~36bp to ~25bp. The custom adapter sequenced used for trimming all the bases extending 5’ was: GTGACTGGAGTTCC-TTGGCACCCGAGAATTCCA.,Next, both data sets from shApoB and miApoB samples were grouped based on the match to the reference sequence and the obtained unique small RNAs were aligned to the sequence of pre-miApoB: GATCCTGGAGGCTTGC-TGAAGGCTGTATGCTGATGGACAGGTCAATCAATCTTGTTTTGGCCACTGACTGACAAGATTGAGACCTGTCCATCAGGACACAAGGCCTGTTACTAGCACTCACATGGAACAAATGGCCCAGATCTGGCCGCAG or shApoB: GATCCCCGATTGATTGACCTGTCCATTTCAAGAGAATGGACAGGTCAATCAATC-TTTTTCAGCTT sequence, respectively.,Supplementary_files_format_and_content: Spreadsheet including reads abundancy. Figure 1 and showing alliingment with references miApoB and shApoB sequences,Genome_build: miRBase Release 18: November 2011
HEK293T cells were transfected with 4 µg shApoB- or miApoB-expression plasmids using Lipofectamine 2000 reagent using manufacturers protocol and total RNA was isolated from cells 48 hr post-transfection using Trizol. Small RNA sequencing libraries were generated using high-quality total RNA as input and the NEXTflex Small RNA Sequencing kit (Bioo Scientific, USA). Briefly, the small RNA species were subjected to ligation with 3' and 5' RNA adapters, first strand reverse transcription, and PCR amplification. Sample-specific barcodes were introduced in the PCR step. The PCR products were separated on TBE-PAGE electrophoresis and the expected band around 140-160bp was recovered for each sample. The libraries were multiplexed, clustered, and sequenced on an Illumina HiSeq 2000.
GSM957706
Illumina HiSeq 2000
May 15 2019
size fractionation
transcriptomic
RNA-Seq
total RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX158352,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01086232
GSM957706
GSE39187
0.153468
miApoB
Public on Jul 10 2012
Jul 09 2012
9606
miApoB (small RNA)
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX158352
https://www.ncbi.nlm.nih.gov/biosample/SAMN01086232
1
cell type: cord blood mononuclear cells,developmental stage: 18-22 weeks of gestation,karyotype: 47,XX,+21 and 47,XY,+21,sample type: pool of 3 samples
1017, North road, Dongmen
Shenzhen
China
the Second Clinical Medical College of Jinan University
Wuxian,,Li
Illumina Casava 1.7 software was used for basecalling.,Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the Homo sapiens whole genome using SOAP(2.0) with parameters soap -v 0 -r 2 -s 7 -p 7 -a clean.fa -d ref_genome.fa -o match_genome.soap,The mapped sequences were aligned against miRBase17.0, Rfam 10.0 (http://rfam.sanger.ac.uk/), piRNABank (NCBI) and the human genes UCSC annotation hg19 (http://genome.ucsc.edu/). Overlapping annotation sequences from these data were classified as miRNA, tRNA, rRNA, mRNA, snoRNA, snRNA, piRNA or other non-coding RNAs.,Before expression analysis of known miRNAs, the miRNA expression level was normalized by calculating its transcripts parts per million (TPM). The total clone count is the sum of the frequencies of all unique sequences remaining after filtering.,Genome_build: hg19,Supplementary_files_format_and_content: Tab-delimited text files include TPM values or identified novel miRNAs for each Sample.,Supplementary_files_format_and_content: *txt: abundance measurements,Supplementary_files_format_and_content: *nov.txt: identified novel miRNAs
Cord blood mononuclear cells (CBMCs) were separated by a Ficoll-Paque. Total RNA was harvested using Trizol reagent. The 18-30nt small RNA population was isolated by separating 10 μg of total RNA using denaturing polyacrylamide gel electrophoresis (PAGE). The Illumina Small RNA Sample Prep Kit (Cat# FC-102-1009) was used to construct the sequencing libraries.
GSM968720
Illumina HiSeq 2000
May 15 2019
size fractionation
transcriptomic
RNA-Seq
total RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX160492,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01090683
GSM968720
GSE39436
0.318077
Fetal cord blood, Down syndrome
Public on Jul 17 2015
Jul 17 2012
9606
Q058
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX160492
https://www.ncbi.nlm.nih.gov/biosample/SAMN01090683
1
cell type: cord blood mononuclear cells,developmental stage: 18-22 weeks of gestation,karyotype: 46,XX and 46,XY,sample type: pool of 3 samples
1017, North road, Dongmen
Shenzhen
China
the Second Clinical Medical College of Jinan University
Wuxian,,Li
Illumina Casava 1.7 software was used for basecalling.,Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the Homo sapiens whole genome using SOAP(2.0) with parameters soap -v 0 -r 2 -s 7 -p 7 -a clean.fa -d ref_genome.fa -o match_genome.soap,The mapped sequences were aligned against miRBase17.0, Rfam 10.0 (http://rfam.sanger.ac.uk/), piRNABank (NCBI) and the human genes UCSC annotation hg19 (http://genome.ucsc.edu/). Overlapping annotation sequences from these data were classified as miRNA, tRNA, rRNA, mRNA, snoRNA, snRNA, piRNA or other non-coding RNAs.,Before expression analysis of known miRNAs, the miRNA expression level was normalized by calculating its transcripts parts per million (TPM). The total clone count is the sum of the frequencies of all unique sequences remaining after filtering.,Genome_build: hg19,Supplementary_files_format_and_content: Tab-delimited text files include TPM values or identified novel miRNAs for each Sample.,Supplementary_files_format_and_content: *txt: abundance measurements,Supplementary_files_format_and_content: *nov.txt: identified novel miRNAs
Cord blood mononuclear cells (CBMCs) were separated by a Ficoll-Paque. Total RNA was harvested using Trizol reagent. The 18-30nt small RNA population was isolated by separating 10 μg of total RNA using denaturing polyacrylamide gel electrophoresis (PAGE). The Illumina Small RNA Sample Prep Kit (Cat# FC-102-1009) was used to construct the sequencing libraries.
GSM968721
Illumina HiSeq 2000
May 15 2019
size fractionation
transcriptomic
RNA-Seq
total RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX160493,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01090684
GSM968721
GSE39436
0.726103
Fetal cord blood, control
Public on Jul 17 2015
Jul 17 2012
9606
Q119
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX160493
https://www.ncbi.nlm.nih.gov/biosample/SAMN01090684
1
datatype: RnaSeq,datatype description: Sequencing analysis of RNA expression,rnaextract: shortTotal,rnaextract description: Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation,biorep: 087N,088N,088N,087N,labexpid: LID46100,LID46101,LID46100,LID46101,labversion: iIDR,readtype: 1x101,readtype description: Single 101 nt reads,replicate: 3,4,localization: nucleus,localization description: Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA,protocol: CIP-TAP,protocol description: This kind of library was made from RNA < 200 nucleotides that was pre-treated sequentially with Calf Intestinal Alkaline Phosphatase followed by Tobacco Acid Pyrophosphatase. Hence, it will be enriched for capped RNAs.,rnaextract: shortTotal,rnaextract description: Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation,biorep: 087N,088N,labexpid: LID46100,LID46101,labversion: iIDR,readtype: 1x101,readtype description: Single 101 nt reads
300 Pasteur Dr
Stanford
USA
ENCODE DCC
ENCODE,,DCC
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeCshlShortRnaSeq
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeCshlShortRnaSeq
GSM973661
Illumina HiSeq 2000
May 15 2019
cDNA
transcriptomic
RNA-Seq
nuclear RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX171070,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01095659,Named Annotation: NA000016672.1 (GSM973661_hg19_wgEncodeCshlShortRnaSeqA549NucleusShorttotalCiptapMinusRep3.bigWig),Named Annotation: NA000016673.1 (GSM973661_hg19_wgEncodeCshlShortRnaSeqA549NucleusShorttotalCiptapMinusRep4.bigWig),Named Annotation: NA000016674.1 (GSM973661_hg19_wgEncodeCshlShortRnaSeqA549NucleusShorttotalCiptapPlusRep3.bigWig),Named Annotation: NA000016675.1 (GSM973661_hg19_wgEncodeCshlShortRnaSeqA549NucleusShorttotalCiptapPlusRep4.bigWig)
GSM973661
GSE24565
0.119616
A549
Public on Jul 26 2012
Jul 25 2012
9606
CSHL_RnaSeq_A549_nucleus_CIP-TAP_shortTotal
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX171070
https://www.ncbi.nlm.nih.gov/biosample/SAMN01095659
1
datatype: RnaSeq,datatype description: Sequencing analysis of RNA expression,rnaextract: shortTotal,rnaextract description: Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation,biorep: 086N,085N,085N,086N,labexpid: LID46272,LID46273,LID46272,LID46273,labversion: iIDR,readtype: 1x101,readtype description: Single 101 nt reads,replicate: 3,4,localization: nucleus,localization description: Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA,protocol: CIP-TAP,protocol description: This kind of library was made from RNA < 200 nucleotides that was pre-treated sequentially with Calf Intestinal Alkaline Phosphatase followed by Tobacco Acid Pyrophosphatase. Hence, it will be enriched for capped RNAs.,rnaextract: shortTotal,rnaextract description: Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation,biorep: 085N,086N,labexpid: LID46272,LID46273,labversion: iIDR,readtype: 1x101,readtype description: Single 101 nt reads
300 Pasteur Dr
Stanford
USA
ENCODE DCC
ENCODE,,DCC
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeCshlShortRnaSeq
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeCshlShortRnaSeq
GSM973663
Illumina HiSeq 2000
May 15 2019
cDNA
transcriptomic
RNA-Seq
nuclear RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX171072,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01095661,Named Annotation: NA000016678.1 (GSM973663_hg19_wgEncodeCshlShortRnaSeqSknshNucleusShorttotalCiptapMinusRep3.bigWig),Named Annotation: NA000016679.1 (GSM973663_hg19_wgEncodeCshlShortRnaSeqSknshNucleusShorttotalCiptapMinusRep4.bigWig),Named Annotation: NA000016680.1 (GSM973663_hg19_wgEncodeCshlShortRnaSeqSknshNucleusShorttotalCiptapPlusRep3.bigWig),Named Annotation: NA000016681.1 (GSM973663_hg19_wgEncodeCshlShortRnaSeqSknshNucleusShorttotalCiptapPlusRep4.bigWig)
GSM973663
GSE24565
0
SK-N-SH
Public on Jul 26 2012
Jul 25 2012
9606
CSHL_RnaSeq_SK-N-SH_nucleus_CIP-TAP_shortTotal
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX171072
https://www.ncbi.nlm.nih.gov/biosample/SAMN01095661
1
datatype: RnaSeq,datatype description: Sequencing analysis of RNA expression,rnaextract: shortTotal,rnaextract description: Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation,biorep: 087C,087C,088C,088C,labexpid: LID46063,LID46062,LID46063,LID46062,labversion: iIDR,readtype: 1x101,readtype description: Single 101 nt reads,replicate: 3,4,localization: cytosol,localization description: The fluid between the cells outer membrane and the nucleus,protocol: None,protocol description: No special treatment or protocol applies,rnaextract: shortTotal,rnaextract description: Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation,biorep: 087C,088C,labexpid: LID46062,LID46063,labversion: iIDR,readtype: 1x101,readtype description: Single 101 nt reads
300 Pasteur Dr
Stanford
USA
ENCODE DCC
ENCODE,,DCC
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeCshlShortRnaSeq
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeCshlShortRnaSeq
GSM973664
Illumina HiSeq 2000
May 15 2019
cDNA
transcriptomic
RNA-Seq
cytoplasmic RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX171073,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01095662,Named Annotation: NA000016682.1 (GSM973664_hg19_wgEncodeCshlShortRnaSeqA549CytosolShorttotalMinusRep3.bigWig),Named Annotation: NA000016683.1 (GSM973664_hg19_wgEncodeCshlShortRnaSeqA549CytosolShorttotalMinusRep4.bigWig),Named Annotation: NA000016684.1 (GSM973664_hg19_wgEncodeCshlShortRnaSeqA549CytosolShorttotalPlusRep3.bigWig),Named Annotation: NA000016685.1 (GSM973664_hg19_wgEncodeCshlShortRnaSeqA549CytosolShorttotalPlusRep4.bigWig)
GSM973664
GSE24565
0.259662
A549
Public on Jul 26 2012
Jul 25 2012
9606
CSHL_RnaSeq_A549_cytosol_shortTotal
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX171073
https://www.ncbi.nlm.nih.gov/biosample/SAMN01095662
1
datatype: RnaSeq,datatype description: Sequencing analysis of RNA expression,rnaextract: shortTotal,rnaextract description: Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation,biorep: 086N,085N,085N,086N,labexpid: LID46203,LID46204,LID46203,LID46204,labversion: iIDR,readtype: 1x101,readtype description: Single 101 nt reads,replicate: 3,4,localization: nucleus,localization description: Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA,protocol: None,protocol description: No special treatment or protocol applies,rnaextract: shortTotal,rnaextract description: Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation,biorep: 085N,086N,labexpid: LID46203,LID46204,labversion: iIDR,readtype: 1x101,readtype description: Single 101 nt reads
300 Pasteur Dr
Stanford
USA
ENCODE DCC
ENCODE,,DCC
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeCshlShortRnaSeq
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeCshlShortRnaSeq
GSM973665
Illumina HiSeq 2000
May 15 2019
cDNA
transcriptomic
RNA-Seq
nuclear RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX171074,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01095663,Named Annotation: NA000016686.1 (GSM973665_hg19_wgEncodeCshlShortRnaSeqSknshNucleusShorttotalMinusRep3.bigWig),Named Annotation: NA000016687.1 (GSM973665_hg19_wgEncodeCshlShortRnaSeqSknshNucleusShorttotalMinusRep4.bigWig),Named Annotation: NA000016688.1 (GSM973665_hg19_wgEncodeCshlShortRnaSeqSknshNucleusShorttotalPlusRep3.bigWig),Named Annotation: NA000016689.1 (GSM973665_hg19_wgEncodeCshlShortRnaSeqSknshNucleusShorttotalPlusRep4.bigWig)
GSM973665
GSE24565
0
SK-N-SH
Public on Jul 26 2012
Jul 25 2012
9606
CSHL_RnaSeq_SK-N-SH_nucleus_shortTotal
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX171074
https://www.ncbi.nlm.nih.gov/biosample/SAMN01095663
1
datatype: RnaSeq,datatype description: Sequencing analysis of RNA expression,rnaextract: shortTotal,rnaextract description: Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation,biorep: 085C,086C,085C,086C,labexpid: LID46205,LID46205,LID46206,LID46206,labversion: iIDR,readtype: 1x101,readtype description: Single 101 nt reads,replicate: 3,4,localization: cytosol,localization description: The fluid between the cells outer membrane and the nucleus,protocol: None,protocol description: No special treatment or protocol applies,rnaextract: shortTotal,rnaextract description: Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation,biorep: 085C,086C,labexpid: LID46205,LID46206,labversion: iIDR,readtype: 1x101,readtype description: Single 101 nt reads
300 Pasteur Dr
Stanford
USA
ENCODE DCC
ENCODE,,DCC
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeCshlShortRnaSeq
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeCshlShortRnaSeq
GSM973666
Illumina HiSeq 2000
May 15 2019
cDNA
transcriptomic
RNA-Seq
cytoplasmic RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX171075,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01095664,Named Annotation: NA000016690.1 (GSM973666_hg19_wgEncodeCshlShortRnaSeqSknshCytosolShorttotalMinusRep3.bigWig),Named Annotation: NA000016691.1 (GSM973666_hg19_wgEncodeCshlShortRnaSeqSknshCytosolShorttotalMinusRep4.bigWig),Named Annotation: NA000016692.1 (GSM973666_hg19_wgEncodeCshlShortRnaSeqSknshCytosolShorttotalPlusRep3.bigWig),Named Annotation: NA000016693.1 (GSM973666_hg19_wgEncodeCshlShortRnaSeqSknshCytosolShorttotalPlusRep4.bigWig)
GSM973666
GSE24565
0.291806
SK-N-SH
Public on Jul 26 2012
Jul 25 2012
9606
CSHL_RnaSeq_SK-N-SH_cytosol_shortTotal
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX171075
https://www.ncbi.nlm.nih.gov/biosample/SAMN01095664
1
biomaterial_type: immortalized cell line,line: SK-N-SH,datatype: RnaSeq,datatype description: Sequencing analysis of RNA expression,rnaextract: shortTotal,rnaextract description: Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation,biorep: 086WC,085WC,086WC,085WC,labexpid: LID46956,LID46957,LID46957,LID46956,labversion: iIDR,readtype: 1x101,readtype description: Single 101 nt reads,replicate: 3,4,localization: cell,localization description: Whole cell,protocol: TAP-Only,protocol description: This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned.,rnaextract: shortTotal,rnaextract description: Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation,biorep: 085WC,labexpid: LID46956,readtype: 1x101,readtype description: Single 101 nt reads,replicate: 3
300 Pasteur Dr
Stanford
USA
ENCODE DCC
ENCODE,,DCC
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeCshlShortRnaSeq
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeCshlShortRnaSeq
GSM973667
Illumina HiSeq 2000
May 15 2019
cDNA
transcriptomic
RNA-Seq
total RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX171076,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01095665,Named Annotation: NA000016694.1 (GSM973667_hg19_wgEncodeCshlShortRnaSeqSknshCellShorttotalTapMinusRep3.bigWig),Named Annotation: NA000016695.1 (GSM973667_hg19_wgEncodeCshlShortRnaSeqSknshCellShorttotalTapMinusRep4.bigWig),Named Annotation: NA000016696.1 (GSM973667_hg19_wgEncodeCshlShortRnaSeqSknshCellShorttotalTapPlusRep3.bigWig),Named Annotation: NA000016697.1 (GSM973667_hg19_wgEncodeCshlShortRnaSeqSknshCellShorttotalTapPlusRep4.bigWig)
GSM973667
GSE24565
0.225997
SK-N-SH
Public on Jul 26 2012
Jul 25 2012
9606
CSHL_RnaSeq_SK-N-SH_cell_TAP-Only_shortTotal
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX171076
https://www.ncbi.nlm.nih.gov/biosample/SAMN01095665
1
datatype: RnaSeq,datatype description: Sequencing analysis of RNA expression,rnaextract: shortTotal,rnaextract description: Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation,biorep: 087WC,088WC,087WC,088WC,labexpid: LID46058,LID46058,LID46059,LID46059,labversion: iIDR,readtype: 1x101,readtype description: Single 101 nt reads,replicate: 3,4,localization: cell,localization description: Whole cell,protocol: None,protocol description: No special treatment or protocol applies,rnaextract: shortTotal,rnaextract description: Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation,biorep: 087WC,088WC,labexpid: LID46058,LID46059,labversion: iIDR,readtype: 1x101,readtype description: Single 101 nt reads
300 Pasteur Dr
Stanford
USA
ENCODE DCC
ENCODE,,DCC
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeCshlShortRnaSeq
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeCshlShortRnaSeq
GSM973668
Illumina HiSeq 2000
May 15 2019
cDNA
transcriptomic
RNA-Seq
total RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX171077,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01095666,Named Annotation: NA000016698.1 (GSM973668_hg19_wgEncodeCshlShortRnaSeqA549CellShorttotalMinusRep3.bigWig),Named Annotation: NA000016699.1 (GSM973668_hg19_wgEncodeCshlShortRnaSeqA549CellShorttotalMinusRep4.bigWig),Named Annotation: NA000016700.1 (GSM973668_hg19_wgEncodeCshlShortRnaSeqA549CellShorttotalPlusRep3.bigWig),Named Annotation: NA000016701.1 (GSM973668_hg19_wgEncodeCshlShortRnaSeqA549CellShorttotalPlusRep4.bigWig)
GSM973668
GSE24565
0.465479
A549
Public on Jul 26 2012
Jul 25 2012
9606
CSHL_RnaSeq_A549_cell_shortTotal
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX171077
https://www.ncbi.nlm.nih.gov/biosample/SAMN01095666
1
datatype: RnaSeq,datatype description: Sequencing analysis of RNA expression,rnaextract: shortTotal,rnaextract description: Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation,biorep: 087C,087C,088C,088C,labexpid: LID46102,LID46103,LID46102,LID46103,labversion: iIDR,readtype: 1x101,readtype description: Single 101 nt reads,replicate: 3,4,localization: cytosol,localization description: The fluid between the cells outer membrane and the nucleus,protocol: CIP-TAP,protocol description: This kind of library was made from RNA < 200 nucleotides that was pre-treated sequentially with Calf Intestinal Alkaline Phosphatase followed by Tobacco Acid Pyrophosphatase. Hence, it will be enriched for capped RNAs.,rnaextract: shortTotal,rnaextract description: Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation,biorep: 087C,088C,labexpid: LID46102,LID46103,labversion: iIDR,readtype: 1x101,readtype description: Single 101 nt reads
300 Pasteur Dr
Stanford
USA
ENCODE DCC
ENCODE,,DCC
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeCshlShortRnaSeq
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeCshlShortRnaSeq
GSM973669
Illumina HiSeq 2000
May 15 2019
cDNA
transcriptomic
RNA-Seq
cytoplasmic RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX171078,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01095667,Named Annotation: NA000016702.1 (GSM973669_hg19_wgEncodeCshlShortRnaSeqA549CytosolShorttotalCiptapMinusRep3.bigWig),Named Annotation: NA000016703.1 (GSM973669_hg19_wgEncodeCshlShortRnaSeqA549CytosolShorttotalCiptapMinusRep4.bigWig),Named Annotation: NA000016704.1 (GSM973669_hg19_wgEncodeCshlShortRnaSeqA549CytosolShorttotalCiptapPlusRep3.bigWig),Named Annotation: NA000016705.1 (GSM973669_hg19_wgEncodeCshlShortRnaSeqA549CytosolShorttotalCiptapPlusRep4.bigWig)
GSM973669
GSE24565
0.206491
A549
Public on Jul 26 2012
Jul 25 2012
9606
CSHL_RnaSeq_A549_cytosol_CIP-TAP_shortTotal
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX171078
https://www.ncbi.nlm.nih.gov/biosample/SAMN01095667
1
datatype: RnaSeq,datatype description: Sequencing analysis of RNA expression,rnaextract: shortTotal,rnaextract description: Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation,biorep: 045C,046C,046C,045C,labexpid: LID45888,LID45889,LID45888,LID45889,labversion: iIDR,readtype: 1x101,readtype description: Single 101 nt reads,replicate: 1,2,localization: cytosol,localization description: The fluid between the cells outer membrane and the nucleus,protocol: CIP-TAP,protocol description: This kind of library was made from RNA < 200 nucleotides that was pre-treated sequentially with Calf Intestinal Alkaline Phosphatase followed by Tobacco Acid Pyrophosphatase. Hence, it will be enriched for capped RNAs.,rnaextract: shortTotal,rnaextract description: Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation,biorep: 045C,046C,labexpid: LID45888,LID45889,labversion: iIDR,readtype: 1x101,readtype description: Single 101 nt reads
300 Pasteur Dr
Stanford
USA
ENCODE DCC
ENCODE,,DCC
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeCshlShortRnaSeq
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeCshlShortRnaSeq
GSM973670
Illumina HiSeq 2000
May 15 2019
cDNA
transcriptomic
RNA-Seq
cytoplasmic RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX171079,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01095668,Named Annotation: NA000016706.1 (GSM973670_hg19_wgEncodeCshlShortRnaSeqImr90CytosolShorttotalCiptapMinusRep1.bigWig),Named Annotation: NA000016707.1 (GSM973670_hg19_wgEncodeCshlShortRnaSeqImr90CytosolShorttotalCiptapMinusRep2.bigWig),Named Annotation: NA000016708.1 (GSM973670_hg19_wgEncodeCshlShortRnaSeqImr90CytosolShorttotalCiptapPlusRep1.bigWig),Named Annotation: NA000016709.1 (GSM973670_hg19_wgEncodeCshlShortRnaSeqImr90CytosolShorttotalCiptapPlusRep2.bigWig)
GSM973670
GSE24565
0.188175
IMR90
Public on Jul 26 2012
Jul 25 2012
9606
CSHL_RnaSeq_IMR90_cytosol_CIP-TAP_shortTotal
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX171079
https://www.ncbi.nlm.nih.gov/biosample/SAMN01095668
1
datatype: RnaSeq,datatype description: Sequencing analysis of RNA expression,rnaextract: shortTotal,rnaextract description: Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation,biorep: 045C,046C,046C,045C,labexpid: LID45957,LID45958,LID45958,LID45957,labversion: iIDR,readtype: 1x101,readtype description: Single 101 nt reads,replicate: 1,2,localization: cytosol,localization description: The fluid between the cells outer membrane and the nucleus,protocol: None,protocol description: No special treatment or protocol applies,rnaextract: shortTotal,rnaextract description: Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation,biorep: 045C,046C,labexpid: LID45957,LID45958,labversion: iIDR,readtype: 1x101,readtype description: Single 101 nt reads
300 Pasteur Dr
Stanford
USA
ENCODE DCC
ENCODE,,DCC
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeCshlShortRnaSeq
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeCshlShortRnaSeq
GSM973671
Illumina HiSeq 2000
May 15 2019
cDNA
transcriptomic
RNA-Seq
cytoplasmic RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX171080,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01095669,Named Annotation: NA000016710.1 (GSM973671_hg19_wgEncodeCshlShortRnaSeqImr90CytosolShorttotalMinusRep1.bigWig),Named Annotation: NA000016711.1 (GSM973671_hg19_wgEncodeCshlShortRnaSeqImr90CytosolShorttotalMinusRep2.bigWig),Named Annotation: NA000016712.1 (GSM973671_hg19_wgEncodeCshlShortRnaSeqImr90CytosolShorttotalPlusRep1.bigWig),Named Annotation: NA000016713.1 (GSM973671_hg19_wgEncodeCshlShortRnaSeqImr90CytosolShorttotalPlusRep2.bigWig)
GSM973671
GSE24565
0.734997
IMR90
Public on Jul 26 2012
Jul 25 2012
9606
CSHL_RnaSeq_IMR90_cytosol_shortTotal
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX171080
https://www.ncbi.nlm.nih.gov/biosample/SAMN01095669
1
datatype: RnaSeq,datatype description: Sequencing analysis of RNA expression,rnaextract: shortTotal,rnaextract description: Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation,biorep: 089C,090C,089C,090C,labexpid: LID46315,LID46315,LID46316,LID46316,labversion: iIDR,readtype: 1x101,readtype description: Single 101 nt reads,replicate: 3,4,localization: cytosol,localization description: The fluid between the cells outer membrane and the nucleus,protocol: None,protocol description: No special treatment or protocol applies,rnaextract: shortTotal,rnaextract description: Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation,biorep: 089C,090C,labexpid: LID46315,LID46316,labversion: iIDR,readtype: 1x101,readtype description: Single 101 nt reads
300 Pasteur Dr
Stanford
USA
ENCODE DCC
ENCODE,,DCC
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeCshlShortRnaSeq
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeCshlShortRnaSeq
GSM973672
Illumina HiSeq 2000
May 15 2019
cDNA
transcriptomic
RNA-Seq
cytoplasmic RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX171081,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01095670,Named Annotation: NA000016714.1 (GSM973672_hg19_wgEncodeCshlShortRnaSeqMcf7CytosolShorttotalMinusRep3.bigWig),Named Annotation: NA000016715.1 (GSM973672_hg19_wgEncodeCshlShortRnaSeqMcf7CytosolShorttotalMinusRep4.bigWig),Named Annotation: NA000016716.1 (GSM973672_hg19_wgEncodeCshlShortRnaSeqMcf7CytosolShorttotalPlusRep3.bigWig),Named Annotation: NA000016717.1 (GSM973672_hg19_wgEncodeCshlShortRnaSeqMcf7CytosolShorttotalPlusRep4.bigWig)
GSM973672
GSE24565
0.00781
MCF-7
Public on Jul 26 2012
Jul 25 2012
9606
CSHL_RnaSeq_MCF-7_cytosol_shortTotal
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX171081
https://www.ncbi.nlm.nih.gov/biosample/SAMN01095670
1
datatype: RnaSeq,datatype description: Sequencing analysis of RNA expression,rnaextract: shortTotal,rnaextract description: Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation,biorep: 045N,046N,045N,046N,labexpid: LID45886,LID45887,LID45886,LID45887,labversion: iIDR,readtype: 1x101,readtype description: Single 101 nt reads,replicate: 1,2,localization: nucleus,localization description: Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA,protocol: CIP-TAP,protocol description: This kind of library was made from RNA < 200 nucleotides that was pre-treated sequentially with Calf Intestinal Alkaline Phosphatase followed by Tobacco Acid Pyrophosphatase. Hence, it will be enriched for capped RNAs.,rnaextract: shortTotal,rnaextract description: Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation,biorep: 045N,046N,labexpid: LID45886,LID45887,labversion: iIDR,readtype: 1x101,readtype description: Single 101 nt reads
300 Pasteur Dr
Stanford
USA
ENCODE DCC
ENCODE,,DCC
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeCshlShortRnaSeq
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeCshlShortRnaSeq
GSM973673
Illumina HiSeq 2000
May 15 2019
cDNA
transcriptomic
RNA-Seq
nuclear RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX171082,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01095671,Named Annotation: NA000016718.1 (GSM973673_hg19_wgEncodeCshlShortRnaSeqImr90NucleusShorttotalCiptapMinusRep1.bigWig),Named Annotation: NA000016719.1 (GSM973673_hg19_wgEncodeCshlShortRnaSeqImr90NucleusShorttotalCiptapMinusRep2.bigWig),Named Annotation: NA000016720.1 (GSM973673_hg19_wgEncodeCshlShortRnaSeqImr90NucleusShorttotalCiptapPlusRep1.bigWig),Named Annotation: NA000016721.1 (GSM973673_hg19_wgEncodeCshlShortRnaSeqImr90NucleusShorttotalCiptapPlusRep2.bigWig)
GSM973673
GSE24565
0.693657
IMR90
Public on Jul 26 2012
Jul 25 2012
9606
CSHL_RnaSeq_IMR90_nucleus_CIP-TAP_shortTotal
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX171082
https://www.ncbi.nlm.nih.gov/biosample/SAMN01095671
1
datatype: RnaSeq,datatype description: Sequencing analysis of RNA expression,rnaextract: shortTotal,rnaextract description: Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation,biorep: 087WC,088WC,087WC,088WC,labexpid: LID46098,LID46099,LID46098,LID46099,labversion: iIDR,readtype: 1x101,readtype description: Single 101 nt reads,replicate: 3,4,localization: cell,localization description: Whole cell,protocol: CIP-TAP,protocol description: This kind of library was made from RNA < 200 nucleotides that was pre-treated sequentially with Calf Intestinal Alkaline Phosphatase followed by Tobacco Acid Pyrophosphatase. Hence, it will be enriched for capped RNAs.,rnaextract: shortTotal,rnaextract description: Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation,biorep: 087WC,088WC,labexpid: LID46098,LID46099,labversion: iIDR,readtype: 1x101,readtype description: Single 101 nt reads
300 Pasteur Dr
Stanford
USA
ENCODE DCC
ENCODE,,DCC
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeCshlShortRnaSeq
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeCshlShortRnaSeq
GSM973674
Illumina HiSeq 2000
May 15 2019
cDNA
transcriptomic
RNA-Seq
total RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX171083,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01095672,Named Annotation: NA000016722.1 (GSM973674_hg19_wgEncodeCshlShortRnaSeqA549CellShorttotalCiptapMinusRep3.bigWig),Named Annotation: NA000016723.1 (GSM973674_hg19_wgEncodeCshlShortRnaSeqA549CellShorttotalCiptapMinusRep4.bigWig),Named Annotation: NA000016724.1 (GSM973674_hg19_wgEncodeCshlShortRnaSeqA549CellShorttotalCiptapPlusRep3.bigWig),Named Annotation: NA000016725.1 (GSM973674_hg19_wgEncodeCshlShortRnaSeqA549CellShorttotalCiptapPlusRep4.bigWig)
GSM973674
GSE24565
0.378444
A549
Public on Jul 26 2012
Jul 25 2012
9606
CSHL_RnaSeq_A549_cell_CIP-TAP_shortTotal
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX171083
https://www.ncbi.nlm.nih.gov/biosample/SAMN01095672
1
biomaterial_type: immortalized cell line,line: SK-N-SH,datatype: RnaSeq,datatype description: Sequencing analysis of RNA expression,rnaextract: shortTotal,rnaextract description: Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation,biorep: 086WC,085WC,086WC,085WC,labexpid: LID46201,LID46202,LID46201,LID46202,labversion: iIDR,readtype: 1x101,readtype description: Single 101 nt reads,replicate: 3,4,localization: cell,localization description: Whole cell,protocol: None,protocol description: No special treatment or protocol applies,rnaextract: shortTotal,rnaextract description: Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation,biorep: 085WC,086WC,labexpid: LID46201,LID46202,labversion: iIDR,readtype: 1x101,readtype description: Single 101 nt reads
300 Pasteur Dr
Stanford
USA
ENCODE DCC
ENCODE,,DCC
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeCshlShortRnaSeq
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeCshlShortRnaSeq
GSM973675
Illumina HiSeq 2000
May 15 2019
cDNA
transcriptomic
RNA-Seq
total RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX171084,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01095673,Named Annotation: NA000016726.1 (GSM973675_hg19_wgEncodeCshlShortRnaSeqSknshCellShorttotalMinusRep3.bigWig),Named Annotation: NA000016727.1 (GSM973675_hg19_wgEncodeCshlShortRnaSeqSknshCellShorttotalMinusRep4.bigWig),Named Annotation: NA000016728.1 (GSM973675_hg19_wgEncodeCshlShortRnaSeqSknshCellShorttotalPlusRep3.bigWig),Named Annotation: NA000016729.1 (GSM973675_hg19_wgEncodeCshlShortRnaSeqSknshCellShorttotalPlusRep4.bigWig)
GSM973675
GSE24565
0.081978
SK-N-SH
Public on Jul 26 2012
Jul 25 2012
9606
CSHL_RnaSeq_SK-N-SH_cell_shortTotal
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX171084
https://www.ncbi.nlm.nih.gov/biosample/SAMN01095673
1
biomaterial_type: immortalized cell line,line: MCF-7,datatype: RnaSeq,datatype description: Sequencing analysis of RNA expression,rnaextract: shortTotal,rnaextract description: Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation,biorep: 089WC,090WC,089WC,090WC,labexpid: LID46458,LID46459,LID46458,LID46459,labversion: iIDR,readtype: 1x101,readtype description: Single 101 nt reads,replicate: 3,4,localization: cell,localization description: Whole cell,protocol: CIP-TAP,protocol description: This kind of library was made from RNA < 200 nucleotides that was pre-treated sequentially with Calf Intestinal Alkaline Phosphatase followed by Tobacco Acid Pyrophosphatase. Hence, it will be enriched for capped RNAs.,rnaextract: shortTotal,rnaextract description: Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation,biorep: 089WC,090WC,labexpid: LID46458,LID46459,labversion: iIDR,readtype: 1x101,readtype description: Single 101 nt reads
300 Pasteur Dr
Stanford
USA
ENCODE DCC
ENCODE,,DCC
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeCshlShortRnaSeq
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeCshlShortRnaSeq
GSM973676
Illumina HiSeq 2000
May 15 2019
cDNA
transcriptomic
RNA-Seq
total RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX171085,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01095674,Named Annotation: NA000016730.1 (GSM973676_hg19_wgEncodeCshlShortRnaSeqMcf7CellShorttotalCiptapMinusRep3.bigWig),Named Annotation: NA000016731.1 (GSM973676_hg19_wgEncodeCshlShortRnaSeqMcf7CellShorttotalCiptapMinusRep4.bigWig),Named Annotation: NA000016732.1 (GSM973676_hg19_wgEncodeCshlShortRnaSeqMcf7CellShorttotalCiptapPlusRep3.bigWig),Named Annotation: NA000016733.1 (GSM973676_hg19_wgEncodeCshlShortRnaSeqMcf7CellShorttotalCiptapPlusRep4.bigWig)
GSM973676
GSE24565
0.385373
MCF-7
Public on Jul 26 2012
Jul 25 2012
9606
CSHL_RnaSeq_MCF-7_cell_CIP-TAP_shortTotal
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX171085
https://www.ncbi.nlm.nih.gov/biosample/SAMN01095674
1
biomaterial_type: immortalized cell line,line: SK-N-SH,datatype: RnaSeq,datatype description: Sequencing analysis of RNA expression,rnaextract: shortTotal,rnaextract description: Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation,biorep: 086WC,085WC,086WC,085WC,labexpid: LID46270,LID46270,LID46271,LID46271,labversion: iIDR,readtype: 1x101,readtype description: Single 101 nt reads,replicate: 3,4,localization: cell,localization description: Whole cell,protocol: CIP-TAP,protocol description: This kind of library was made from RNA < 200 nucleotides that was pre-treated sequentially with Calf Intestinal Alkaline Phosphatase followed by Tobacco Acid Pyrophosphatase. Hence, it will be enriched for capped RNAs.,rnaextract: shortTotal,rnaextract description: Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation,biorep: 085WC,086WC,labexpid: LID46270,LID46271,labversion: iIDR,readtype: 1x101,readtype description: Single 101 nt reads
300 Pasteur Dr
Stanford
USA
ENCODE DCC
ENCODE,,DCC
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeCshlShortRnaSeq
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeCshlShortRnaSeq
GSM973677
Illumina HiSeq 2000
May 15 2019
cDNA
transcriptomic
RNA-Seq
total RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX171086,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01095675,Named Annotation: NA000016734.1 (GSM973677_hg19_wgEncodeCshlShortRnaSeqSknshCellShorttotalCiptapMinusRep3.bigWig),Named Annotation: NA000016735.1 (GSM973677_hg19_wgEncodeCshlShortRnaSeqSknshCellShorttotalCiptapMinusRep4.bigWig),Named Annotation: NA000016736.1 (GSM973677_hg19_wgEncodeCshlShortRnaSeqSknshCellShorttotalCiptapPlusRep3.bigWig),Named Annotation: NA000016737.1 (GSM973677_hg19_wgEncodeCshlShortRnaSeqSknshCellShorttotalCiptapPlusRep4.bigWig)
GSM973677
GSE24565
0.188249
SK-N-SH
Public on Jul 26 2012
Jul 25 2012
9606
CSHL_RnaSeq_SK-N-SH_cell_CIP-TAP_shortTotal
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX171086
https://www.ncbi.nlm.nih.gov/biosample/SAMN01095675
1
datatype: RnaSeq,datatype description: Sequencing analysis of RNA expression,rnaextract: shortTotal,rnaextract description: Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation,biorep: 045N,046N,045N,046N,labexpid: LID45955,LID45956,LID45955,LID45956,labversion: iIDR,readtype: 1x101,readtype description: Single 101 nt reads,replicate: 1,2,localization: nucleus,localization description: Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA,protocol: None,protocol description: No special treatment or protocol applies,rnaextract: shortTotal,rnaextract description: Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation,biorep: 045N,046N,labexpid: LID45955,LID45956,labversion: iIDR,readtype: 1x101,readtype description: Single 101 nt reads
300 Pasteur Dr
Stanford
USA
ENCODE DCC
ENCODE,,DCC
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeCshlShortRnaSeq
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeCshlShortRnaSeq
GSM973678
Illumina HiSeq 2000
May 15 2019
cDNA
transcriptomic
RNA-Seq
nuclear RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX171087,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01095676,Named Annotation: NA000016738.1 (GSM973678_hg19_wgEncodeCshlShortRnaSeqImr90NucleusShorttotalMinusRep1.bigWig),Named Annotation: NA000016739.1 (GSM973678_hg19_wgEncodeCshlShortRnaSeqImr90NucleusShorttotalMinusRep2.bigWig),Named Annotation: NA000016740.1 (GSM973678_hg19_wgEncodeCshlShortRnaSeqImr90NucleusShorttotalPlusRep1.bigWig),Named Annotation: NA000016741.1 (GSM973678_hg19_wgEncodeCshlShortRnaSeqImr90NucleusShorttotalPlusRep2.bigWig)
GSM973678
GSE24565
0.673594
IMR90
Public on Jul 26 2012
Jul 25 2012
9606
CSHL_RnaSeq_IMR90_nucleus_shortTotal
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX171087
https://www.ncbi.nlm.nih.gov/biosample/SAMN01095676
1
datatype: RnaSeq,datatype description: Sequencing analysis of RNA expression,rnaextract: shortTotal,rnaextract description: Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation,biorep: 045N,046N,045N,046N,labexpid: LID47266,LID47267,LID47266,LID47267,labversion: iIDR,readtype: 1x101,readtype description: Single 101 nt reads,replicate: 1,2,localization: nucleus,localization description: Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA,protocol: TAP-Only,protocol description: This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned.,rnaextract: shortTotal,rnaextract description: Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation,biorep: 045N,labexpid: LID47266,readtype: 1x101,readtype description: Single 101 nt reads,replicate: 1
300 Pasteur Dr
Stanford
USA
ENCODE DCC
ENCODE,,DCC
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeCshlShortRnaSeq
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeCshlShortRnaSeq
GSM973679
Illumina HiSeq 2000
May 15 2019
cDNA
transcriptomic
RNA-Seq
nuclear RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX171088,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01095677,Named Annotation: NA000016742.1 (GSM973679_hg19_wgEncodeCshlShortRnaSeqImr90NucleusShorttotalTapMinusRep1.bigWig),Named Annotation: NA000016743.1 (GSM973679_hg19_wgEncodeCshlShortRnaSeqImr90NucleusShorttotalTapMinusRep2.bigWig),Named Annotation: NA000016744.1 (GSM973679_hg19_wgEncodeCshlShortRnaSeqImr90NucleusShorttotalTapPlusRep1.bigWig),Named Annotation: NA000016745.1 (GSM973679_hg19_wgEncodeCshlShortRnaSeqImr90NucleusShorttotalTapPlusRep2.bigWig)
GSM973679
GSE24565
0.132054
IMR90
Public on Jul 26 2012
Jul 25 2012
9606
CSHL_RnaSeq_IMR90_nucleus_TAP-Only_shortTotal
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX171088
https://www.ncbi.nlm.nih.gov/biosample/SAMN01095677
1
datatype: RnaSeq,datatype description: Sequencing analysis of RNA expression,rnaextract: shortTotal,rnaextract description: Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation,biorep: 045WC,045WC,046WC,046WC,labexpid: LID47262,LID47263,LID47262,LID47263,labversion: iIDR,readtype: 1x101,readtype description: Single 101 nt reads,replicate: 1,2,localization: cell,localization description: Whole cell,protocol: TAP-Only,protocol description: This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned.,rnaextract: shortTotal,rnaextract description: Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation,biorep: 045WC,labexpid: LID47262,readtype: 1x101,readtype description: Single 101 nt reads,replicate: 1
300 Pasteur Dr
Stanford
USA
ENCODE DCC
ENCODE,,DCC
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeCshlShortRnaSeq
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeCshlShortRnaSeq
GSM973680
Illumina HiSeq 2000
May 15 2019
cDNA
transcriptomic
RNA-Seq
total RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX171089,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01095678,Named Annotation: NA000016746.1 (GSM973680_hg19_wgEncodeCshlShortRnaSeqImr90CellShorttotalTapMinusRep1.bigWig),Named Annotation: NA000016747.1 (GSM973680_hg19_wgEncodeCshlShortRnaSeqImr90CellShorttotalTapMinusRep2.bigWig),Named Annotation: NA000016748.1 (GSM973680_hg19_wgEncodeCshlShortRnaSeqImr90CellShorttotalTapPlusRep1.bigWig),Named Annotation: NA000016749.1 (GSM973680_hg19_wgEncodeCshlShortRnaSeqImr90CellShorttotalTapPlusRep2.bigWig)
GSM973680
GSE24565
0.378901
IMR90
Public on Jul 26 2012
Jul 25 2012
9606
CSHL_RnaSeq_IMR90_cell_TAP-Only_shortTotal
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX171089
https://www.ncbi.nlm.nih.gov/biosample/SAMN01095678
1
datatype: RnaSeq,datatype description: Sequencing analysis of RNA expression,rnaextract: shortTotal,rnaextract description: Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation,biorep: 089C,090C,089C,090C,labexpid: LID47163,LID47162,LID47162,LID47163,labversion: iIDR,readtype: 1x101,readtype description: Single 101 nt reads,replicate: 3,4,localization: cytosol,localization description: The fluid between the cells outer membrane and the nucleus,protocol: TAP-Only,protocol description: This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned.,rnaextract: shortTotal,rnaextract description: Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation,biorep: 089C,labexpid: LID47162,readtype: 1x101,readtype description: Single 101 nt reads,replicate: 3
300 Pasteur Dr
Stanford
USA
ENCODE DCC
ENCODE,,DCC
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeCshlShortRnaSeq
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeCshlShortRnaSeq
GSM973681
Illumina HiSeq 2000
May 15 2019
cDNA
transcriptomic
RNA-Seq
cytoplasmic RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX171090,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01095679,Named Annotation: NA000016750.1 (GSM973681_hg19_wgEncodeCshlShortRnaSeqMcf7CytosolShorttotalTapMinusRep3.bigWig),Named Annotation: NA000016751.1 (GSM973681_hg19_wgEncodeCshlShortRnaSeqMcf7CytosolShorttotalTapMinusRep4.bigWig),Named Annotation: NA000016752.1 (GSM973681_hg19_wgEncodeCshlShortRnaSeqMcf7CytosolShorttotalTapPlusRep3.bigWig),Named Annotation: NA000016753.1 (GSM973681_hg19_wgEncodeCshlShortRnaSeqMcf7CytosolShorttotalTapPlusRep4.bigWig)
GSM973681
GSE24565
0.219036
MCF-7
Public on Jul 26 2012
Jul 25 2012
9606
CSHL_RnaSeq_MCF-7_cytosol_TAP-Only_shortTotal
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX171090
https://www.ncbi.nlm.nih.gov/biosample/SAMN01095679
1
datatype: RnaSeq,datatype description: Sequencing analysis of RNA expression,rnaextract: shortTotal,rnaextract description: Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation,biorep: 089N,090N,089N,090N,labexpid: LID47165,LID47164,LID47164,LID47165,labversion: iIDR,readtype: 1x101,readtype description: Single 101 nt reads,replicate: 3,4,localization: nucleus,localization description: Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA,protocol: TAP-Only,protocol description: This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned.,rnaextract: shortTotal,rnaextract description: Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation,biorep: 089N,labexpid: LID47164,readtype: 1x101,readtype description: Single 101 nt reads,replicate: 3
300 Pasteur Dr
Stanford
USA
ENCODE DCC
ENCODE,,DCC
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeCshlShortRnaSeq
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeCshlShortRnaSeq
GSM973682
Illumina HiSeq 2000
May 15 2019
cDNA
transcriptomic
RNA-Seq
nuclear RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX171091,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01095680,Named Annotation: NA000016754.1 (GSM973682_hg19_wgEncodeCshlShortRnaSeqMcf7NucleusShorttotalTapMinusRep3.bigWig),Named Annotation: NA000016755.1 (GSM973682_hg19_wgEncodeCshlShortRnaSeqMcf7NucleusShorttotalTapMinusRep4.bigWig),Named Annotation: NA000016756.1 (GSM973682_hg19_wgEncodeCshlShortRnaSeqMcf7NucleusShorttotalTapPlusRep3.bigWig),Named Annotation: NA000016757.1 (GSM973682_hg19_wgEncodeCshlShortRnaSeqMcf7NucleusShorttotalTapPlusRep4.bigWig)
GSM973682
GSE24565
0
MCF-7
Public on Jul 26 2012
Jul 25 2012
9606
CSHL_RnaSeq_MCF-7_nucleus_TAP-Only_shortTotal
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX171091
https://www.ncbi.nlm.nih.gov/biosample/SAMN01095680
1
datatype: RnaSeq,datatype description: Sequencing analysis of RNA expression,rnaextract: shortTotal,rnaextract description: Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation,biorep: 087N,088N,088N,087N,labexpid: LID46061,LID46060,LID46060,LID46061,labversion: iIDR,readtype: 1x101,readtype description: Single 101 nt reads,replicate: 3,4,localization: nucleus,localization description: Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA,protocol: None,protocol description: No special treatment or protocol applies,rnaextract: shortTotal,rnaextract description: Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation,biorep: 087N,088N,labexpid: LID46060,LID46061,labversion: iIDR,readtype: 1x101,readtype description: Single 101 nt reads
300 Pasteur Dr
Stanford
USA
ENCODE DCC
ENCODE,,DCC
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeCshlShortRnaSeq
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeCshlShortRnaSeq
GSM973683
Illumina HiSeq 2000
May 15 2019
cDNA
transcriptomic
RNA-Seq
nuclear RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX171092,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01095681,Named Annotation: NA000016758.1 (GSM973683_hg19_wgEncodeCshlShortRnaSeqA549NucleusShorttotalMinusRep3.bigWig),Named Annotation: NA000016759.1 (GSM973683_hg19_wgEncodeCshlShortRnaSeqA549NucleusShorttotalMinusRep4.bigWig),Named Annotation: NA000016760.1 (GSM973683_hg19_wgEncodeCshlShortRnaSeqA549NucleusShorttotalPlusRep3.bigWig),Named Annotation: NA000016761.1 (GSM973683_hg19_wgEncodeCshlShortRnaSeqA549NucleusShorttotalPlusRep4.bigWig)
GSM973683
GSE24565
0.014802
A549
Public on Jul 26 2012
Jul 25 2012
9606
CSHL_RnaSeq_A549_nucleus_shortTotal
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX171092
https://www.ncbi.nlm.nih.gov/biosample/SAMN01095681
1
datatype: RnaSeq,datatype description: Sequencing analysis of RNA expression,rnaextract: shortTotal,rnaextract description: Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation,biorep: 087C,087C,088C,088C,labexpid: LID47041,LID47042,LID47041,LID47042,labversion: iIDR,readtype: 1x101,readtype description: Single 101 nt reads,replicate: 3,4,localization: cytosol,localization description: The fluid between the cells outer membrane and the nucleus,protocol: TAP-Only,protocol description: This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned.,rnaextract: shortTotal,rnaextract description: Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation,biorep: 087C,labexpid: LID47041,readtype: 1x101,readtype description: Single 101 nt reads,replicate: 3
300 Pasteur Dr
Stanford
USA
ENCODE DCC
ENCODE,,DCC
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeCshlShortRnaSeq
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeCshlShortRnaSeq
GSM973684
Illumina HiSeq 2000
May 15 2019
cDNA
transcriptomic
RNA-Seq
cytoplasmic RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX171093,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01095682,Named Annotation: NA000016762.1 (GSM973684_hg19_wgEncodeCshlShortRnaSeqA549CytosolShorttotalTapMinusRep3.bigWig),Named Annotation: NA000016763.1 (GSM973684_hg19_wgEncodeCshlShortRnaSeqA549CytosolShorttotalTapMinusRep4.bigWig),Named Annotation: NA000016764.1 (GSM973684_hg19_wgEncodeCshlShortRnaSeqA549CytosolShorttotalTapPlusRep3.bigWig),Named Annotation: NA000016765.1 (GSM973684_hg19_wgEncodeCshlShortRnaSeqA549CytosolShorttotalTapPlusRep4.bigWig)
GSM973684
GSE24565
0.236536
A549
Public on Jul 26 2012
Jul 25 2012
9606
CSHL_RnaSeq_A549_cytosol_TAP-Only_shortTotal
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX171093
https://www.ncbi.nlm.nih.gov/biosample/SAMN01095682
1
datatype: RnaSeq,datatype description: Sequencing analysis of RNA expression,rnaextract: shortTotal,rnaextract description: Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation,biorep: 088N,087N,088N,087N,labexpid: LID47044,LID47043,LID47044,LID47043,labversion: iIDR,readtype: 1x101,readtype description: Single 101 nt reads,replicate: 3,4,localization: nucleus,localization description: Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA,protocol: TAP-Only,protocol description: This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned.,rnaextract: shortTotal,rnaextract description: Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation,biorep: 087N,labexpid: LID47043,readtype: 1x101,readtype description: Single 101 nt reads,replicate: 3
300 Pasteur Dr
Stanford
USA
ENCODE DCC
ENCODE,,DCC
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeCshlShortRnaSeq
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeCshlShortRnaSeq
GSM973685
Illumina HiSeq 2000
May 15 2019
cDNA
transcriptomic
RNA-Seq
nuclear RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX171094,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01095683,Named Annotation: NA000016766.1 (GSM973685_hg19_wgEncodeCshlShortRnaSeqA549NucleusShorttotalTapMinusRep3.bigWig),Named Annotation: NA000016767.1 (GSM973685_hg19_wgEncodeCshlShortRnaSeqA549NucleusShorttotalTapMinusRep4.bigWig),Named Annotation: NA000016768.1 (GSM973685_hg19_wgEncodeCshlShortRnaSeqA549NucleusShorttotalTapPlusRep3.bigWig),Named Annotation: NA000016769.1 (GSM973685_hg19_wgEncodeCshlShortRnaSeqA549NucleusShorttotalTapPlusRep4.bigWig)
GSM973685
GSE24565
0.100626
A549
Public on Jul 26 2012
Jul 25 2012
9606
CSHL_RnaSeq_A549_nucleus_TAP-Only_shortTotal
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX171094
https://www.ncbi.nlm.nih.gov/biosample/SAMN01095683
1
datatype: RnaSeq,datatype description: Sequencing analysis of RNA expression,rnaextract: shortTotal,rnaextract description: Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation,biorep: 045C,046C,046C,045C,labexpid: LID47264,LID47265,LID47264,LID47265,labversion: iIDR,readtype: 1x101,readtype description: Single 101 nt reads,replicate: 1,2,localization: cytosol,localization description: The fluid between the cells outer membrane and the nucleus,protocol: TAP-Only,protocol description: This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned.,rnaextract: shortTotal,rnaextract description: Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation,biorep: 045C,labexpid: LID47264,readtype: 1x101,readtype description: Single 101 nt reads,replicate: 1
300 Pasteur Dr
Stanford
USA
ENCODE DCC
ENCODE,,DCC
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeCshlShortRnaSeq
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeCshlShortRnaSeq
GSM973686
Illumina HiSeq 2000
May 15 2019
cDNA
transcriptomic
RNA-Seq
cytoplasmic RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX171095,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01095684,Named Annotation: NA000016770.1 (GSM973686_hg19_wgEncodeCshlShortRnaSeqImr90CytosolShorttotalTapMinusRep1.bigWig),Named Annotation: NA000016771.1 (GSM973686_hg19_wgEncodeCshlShortRnaSeqImr90CytosolShorttotalTapMinusRep2.bigWig),Named Annotation: NA000016772.1 (GSM973686_hg19_wgEncodeCshlShortRnaSeqImr90CytosolShorttotalTapPlusRep1.bigWig),Named Annotation: NA000016773.1 (GSM973686_hg19_wgEncodeCshlShortRnaSeqImr90CytosolShorttotalTapPlusRep2.bigWig)
GSM973686
GSE24565
0.150651
IMR90
Public on Jul 26 2012
Jul 25 2012
9606
CSHL_RnaSeq_IMR90_cytosol_TAP-Only_shortTotal
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX171095
https://www.ncbi.nlm.nih.gov/biosample/SAMN01095684
1
datatype: RnaSeq,datatype description: Sequencing analysis of RNA expression,rnaextract: shortTotal,rnaextract description: Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation,biorep: 089N,090N,089N,090N,labexpid: LID46313,LID46313,LID46314,LID46314,labversion: iIDR,readtype: 1x101,readtype description: Single 101 nt reads,replicate: 3,4,localization: nucleus,localization description: Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA,protocol: None,protocol description: No special treatment or protocol applies,rnaextract: shortTotal,rnaextract description: Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation,biorep: 089N,090N,labexpid: LID46313,LID46314,labversion: iIDR,readtype: 1x101,readtype description: Single 101 nt reads
300 Pasteur Dr
Stanford
USA
ENCODE DCC
ENCODE,,DCC
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeCshlShortRnaSeq
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeCshlShortRnaSeq
GSM973687
Illumina HiSeq 2000
May 15 2019
cDNA
transcriptomic
RNA-Seq
nuclear RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX171096,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01095685,Named Annotation: NA000016774.1 (GSM973687_hg19_wgEncodeCshlShortRnaSeqMcf7NucleusShorttotalMinusRep3.bigWig),Named Annotation: NA000016775.1 (GSM973687_hg19_wgEncodeCshlShortRnaSeqMcf7NucleusShorttotalMinusRep4.bigWig),Named Annotation: NA000016776.1 (GSM973687_hg19_wgEncodeCshlShortRnaSeqMcf7NucleusShorttotalPlusRep3.bigWig),Named Annotation: NA000016777.1 (GSM973687_hg19_wgEncodeCshlShortRnaSeqMcf7NucleusShorttotalPlusRep4.bigWig)
GSM973687
GSE24565
0.002195
MCF-7
Public on Jul 26 2012
Jul 25 2012
9606
CSHL_RnaSeq_MCF-7_nucleus_shortTotal
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX171096
https://www.ncbi.nlm.nih.gov/biosample/SAMN01095685
1
datatype: RnaSeq,datatype description: Sequencing analysis of RNA expression,rnaextract: shortTotal,rnaextract description: Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation,biorep: 085C,085C,086C,086C,labexpid: LID46959,LID46958,LID46958,LID46959,labversion: iIDR,readtype: 1x101,readtype description: Single 101 nt reads,replicate: 3,4,localization: cytosol,localization description: The fluid between the cells outer membrane and the nucleus,protocol: TAP-Only,protocol description: This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned.,rnaextract: shortTotal,rnaextract description: Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation,biorep: 085C,labexpid: LID46958,readtype: 1x101,readtype description: Single 101 nt reads,replicate: 3
300 Pasteur Dr
Stanford
USA
ENCODE DCC
ENCODE,,DCC
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeCshlShortRnaSeq
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeCshlShortRnaSeq
GSM973688
Illumina HiSeq 2000
May 15 2019
cDNA
transcriptomic
RNA-Seq
cytoplasmic RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX171097,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01095686,Named Annotation: NA000016778.1 (GSM973688_hg19_wgEncodeCshlShortRnaSeqSknshCytosolShorttotalTapMinusRep3.bigWig),Named Annotation: NA000016779.1 (GSM973688_hg19_wgEncodeCshlShortRnaSeqSknshCytosolShorttotalTapMinusRep4.bigWig),Named Annotation: NA000016780.1 (GSM973688_hg19_wgEncodeCshlShortRnaSeqSknshCytosolShorttotalTapPlusRep3.bigWig),Named Annotation: NA000016781.1 (GSM973688_hg19_wgEncodeCshlShortRnaSeqSknshCytosolShorttotalTapPlusRep4.bigWig)
GSM973688
GSE24565
0.30161
SK-N-SH
Public on Jul 26 2012
Jul 25 2012
9606
CSHL_RnaSeq_SK-N-SH_cytosol_TAP-Only_shortTotal
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX171097
https://www.ncbi.nlm.nih.gov/biosample/SAMN01095686
1
datatype: RnaSeq,datatype description: Sequencing analysis of RNA expression,rnaextract: shortTotal,rnaextract description: Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation,biorep: 086N,085N,085N,086N,labexpid: LID46960,LID46961,LID46960,LID46961,labversion: iIDR,readtype: 1x101,readtype description: Single 101 nt reads,replicate: 3,4,localization: nucleus,localization description: Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA,protocol: TAP-Only,protocol description: This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned.,rnaextract: shortTotal,rnaextract description: Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation,biorep: 085N,labexpid: LID46960,readtype: 1x101,readtype description: Single 101 nt reads,replicate: 3
300 Pasteur Dr
Stanford
USA
ENCODE DCC
ENCODE,,DCC
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeCshlShortRnaSeq
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeCshlShortRnaSeq
GSM973689
Illumina HiSeq 2000
May 15 2019
cDNA
transcriptomic
RNA-Seq
nuclear RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX171098,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01095687,Named Annotation: NA000016782.1 (GSM973689_hg19_wgEncodeCshlShortRnaSeqSknshNucleusShorttotalTapMinusRep3.bigWig),Named Annotation: NA000016783.1 (GSM973689_hg19_wgEncodeCshlShortRnaSeqSknshNucleusShorttotalTapMinusRep4.bigWig),Named Annotation: NA000016784.1 (GSM973689_hg19_wgEncodeCshlShortRnaSeqSknshNucleusShorttotalTapPlusRep3.bigWig),Named Annotation: NA000016785.1 (GSM973689_hg19_wgEncodeCshlShortRnaSeqSknshNucleusShorttotalTapPlusRep4.bigWig)
GSM973689
GSE24565
0.019127
SK-N-SH
Public on Jul 26 2012
Jul 25 2012
9606
CSHL_RnaSeq_SK-N-SH_nucleus_TAP-Only_shortTotal
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX171098
https://www.ncbi.nlm.nih.gov/biosample/SAMN01095687
1
biomaterial_type: immortalized cell line,line: MCF-7,datatype: RnaSeq,datatype description: Sequencing analysis of RNA expression,rnaextract: shortTotal,rnaextract description: Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation,biorep: 089WC,090WC,089WC,090WC,labexpid: LID46312,LID46311,LID46311,LID46312,labversion: iIDR,readtype: 1x101,readtype description: Single 101 nt reads,replicate: 3,4,localization: cell,localization description: Whole cell,protocol: None,protocol description: No special treatment or protocol applies,rnaextract: shortTotal,rnaextract description: Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation,biorep: 089WC,090WC,labexpid: LID46311,LID46312,labversion: iIDR,readtype: 1x101,readtype description: Single 101 nt reads
300 Pasteur Dr
Stanford
USA
ENCODE DCC
ENCODE,,DCC
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeCshlShortRnaSeq
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeCshlShortRnaSeq
GSM973690
Illumina HiSeq 2000
May 15 2019
cDNA
transcriptomic
RNA-Seq
total RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX171099,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01095688,Named Annotation: NA000016786.1 (GSM973690_hg19_wgEncodeCshlShortRnaSeqMcf7CellShorttotalMinusRep3.bigWig),Named Annotation: NA000016787.1 (GSM973690_hg19_wgEncodeCshlShortRnaSeqMcf7CellShorttotalMinusRep4.bigWig),Named Annotation: NA000016788.1 (GSM973690_hg19_wgEncodeCshlShortRnaSeqMcf7CellShorttotalPlusRep3.bigWig),Named Annotation: NA000016789.1 (GSM973690_hg19_wgEncodeCshlShortRnaSeqMcf7CellShorttotalPlusRep4.bigWig)
GSM973690
GSE24565
0
MCF-7
Public on Jul 26 2012
Jul 25 2012
9606
CSHL_RnaSeq_MCF-7_cell_shortTotal
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX171099
https://www.ncbi.nlm.nih.gov/biosample/SAMN01095688
1
datatype: RnaSeq,datatype description: Sequencing analysis of RNA expression,rnaextract: shortTotal,rnaextract description: Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation,biorep: 045WC,045WC,046WC,046WC,labexpid: LID45107,LID45107,LID45110,LID45110,labversion: iIDR,readtype: 1x101,readtype description: Single 101 nt reads,replicate: 1,2,localization: cell,localization description: Whole cell,protocol: None,protocol description: No special treatment or protocol applies,rnaextract: shortTotal,rnaextract description: Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation,biorep: 045WC,046WC,labexpid: LID45107,LID45110,labversion: iIDR,readtype: 1x101,readtype description: Single 101 nt reads
300 Pasteur Dr
Stanford
USA
ENCODE DCC
ENCODE,,DCC
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeCshlShortRnaSeq
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeCshlShortRnaSeq
GSM973691
Illumina HiSeq 2000
May 15 2019
cDNA
transcriptomic
RNA-Seq
total RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX171100,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01095689,Named Annotation: NA000016790.1 (GSM973691_hg19_wgEncodeCshlShortRnaSeqImr90CellShorttotalMinusRep1.bigWig),Named Annotation: NA000016791.1 (GSM973691_hg19_wgEncodeCshlShortRnaSeqImr90CellShorttotalMinusRep2.bigWig),Named Annotation: NA000016792.1 (GSM973691_hg19_wgEncodeCshlShortRnaSeqImr90CellShorttotalPlusRep1.bigWig),Named Annotation: NA000016793.1 (GSM973691_hg19_wgEncodeCshlShortRnaSeqImr90CellShorttotalPlusRep2.bigWig)
GSM973691
GSE24565
0.247878
IMR90
Public on Jul 26 2012
Jul 25 2012
9606
CSHL_RnaSeq_IMR90_cell_shortTotal
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX171100
https://www.ncbi.nlm.nih.gov/biosample/SAMN01095689
1
datatype: RnaSeq,datatype description: Sequencing analysis of RNA expression,rnaextract: shortTotal,rnaextract description: Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation,biorep: 085C,086C,085C,086C,labexpid: LID46274,LID46275,LID46274,LID46275,labversion: iIDR,readtype: 1x101,readtype description: Single 101 nt reads,replicate: 3,4,localization: cytosol,localization description: The fluid between the cells outer membrane and the nucleus,protocol: CIP-TAP,protocol description: This kind of library was made from RNA < 200 nucleotides that was pre-treated sequentially with Calf Intestinal Alkaline Phosphatase followed by Tobacco Acid Pyrophosphatase. Hence, it will be enriched for capped RNAs.,rnaextract: shortTotal,rnaextract description: Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation,biorep: 085C,086C,labexpid: LID46274,LID46275,labversion: iIDR,readtype: 1x101,readtype description: Single 101 nt reads
300 Pasteur Dr
Stanford
USA
ENCODE DCC
ENCODE,,DCC
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeCshlShortRnaSeq
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeCshlShortRnaSeq
GSM973692
Illumina HiSeq 2000
May 15 2019
cDNA
transcriptomic
RNA-Seq
cytoplasmic RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX171101,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01095690,Named Annotation: NA000016794.1 (GSM973692_hg19_wgEncodeCshlShortRnaSeqSknshCytosolShorttotalCiptapMinusRep3.bigWig),Named Annotation: NA000016795.1 (GSM973692_hg19_wgEncodeCshlShortRnaSeqSknshCytosolShorttotalCiptapMinusRep4.bigWig),Named Annotation: NA000016796.1 (GSM973692_hg19_wgEncodeCshlShortRnaSeqSknshCytosolShorttotalCiptapPlusRep3.bigWig),Named Annotation: NA000016797.1 (GSM973692_hg19_wgEncodeCshlShortRnaSeqSknshCytosolShorttotalCiptapPlusRep4.bigWig)
GSM973692
GSE24565
0.436538
SK-N-SH
Public on Jul 26 2012
Jul 25 2012
9606
CSHL_RnaSeq_SK-N-SH_cytosol_CIP-TAP_shortTotal
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX171101
https://www.ncbi.nlm.nih.gov/biosample/SAMN01095690
1
datatype: RnaSeq,datatype description: Sequencing analysis of RNA expression,rnaextract: shortTotal,rnaextract description: Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation,biorep: 045WC,045WC,046WC,046WC,labexpid: LID45108,LID45111,LID45111,LID45108,labversion: iIDR,readtype: 1x101,readtype description: Single 101 nt reads,replicate: 1,2,localization: cell,localization description: Whole cell,protocol: CIP-TAP,protocol description: This kind of library was made from RNA < 200 nucleotides that was pre-treated sequentially with Calf Intestinal Alkaline Phosphatase followed by Tobacco Acid Pyrophosphatase. Hence, it will be enriched for capped RNAs.,rnaextract: shortTotal,rnaextract description: Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation,biorep: 045WC,046WC,labexpid: LID45108,LID45111,labversion: iIDR,readtype: 1x101,readtype description: Single 101 nt reads
300 Pasteur Dr
Stanford
USA
ENCODE DCC
ENCODE,,DCC
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeCshlShortRnaSeq
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeCshlShortRnaSeq
GSM973693
Illumina HiSeq 2000
May 15 2019
cDNA
transcriptomic
RNA-Seq
total RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX171102,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01095691,Named Annotation: NA000016798.1 (GSM973693_hg19_wgEncodeCshlShortRnaSeqImr90CellShorttotalCiptapMinusRep1.bigWig),Named Annotation: NA000016799.1 (GSM973693_hg19_wgEncodeCshlShortRnaSeqImr90CellShorttotalCiptapMinusRep2.bigWig),Named Annotation: NA000016800.1 (GSM973693_hg19_wgEncodeCshlShortRnaSeqImr90CellShorttotalCiptapPlusRep1.bigWig),Named Annotation: NA000016801.1 (GSM973693_hg19_wgEncodeCshlShortRnaSeqImr90CellShorttotalCiptapPlusRep2.bigWig)
GSM973693
GSE24565
0.169463
IMR90
Public on Jul 26 2012
Jul 25 2012
9606
CSHL_RnaSeq_IMR90_cell_CIP-TAP_shortTotal
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX171102
https://www.ncbi.nlm.nih.gov/biosample/SAMN01095691
1
datatype: RnaSeq,datatype description: Sequencing analysis of RNA expression,rnaextract: shortTotal,rnaextract description: Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation,biorep: 067WC,068WC,068WC,067WC,labexpid: LID47658,LID47659,LID47659,LID47658,readtype: 1x101,readtype description: Single 101 nt reads,replicate: 1,2,cell sex: B,localization: cell,localization description: Whole cell,protocol: TAP-Only,protocol description: This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned.,rnaextract: shortTotal,rnaextract description: Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation,biorep: 067WC,068WC,labexpid: LID47658,LID47659,readtype: 1x101,readtype description: Single 101 nt reads
300 Pasteur Dr
Stanford
USA
ENCODE DCC
ENCODE,,DCC
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeCshlShortRnaSeq
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeCshlShortRnaSeq
GSM977028
Illumina HiSeq 2000
May 15 2019
cDNA
transcriptomic
RNA-Seq
total RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX171103,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01095692,Named Annotation: NA000016802.1 (GSM977028_hg19_wgEncodeCshlShortRnaSeqHmscbmCellTapMinusRawRep1.bigWig),Named Annotation: NA000016803.1 (GSM977028_hg19_wgEncodeCshlShortRnaSeqHmscbmCellTapMinusRawRep2.bigWig),Named Annotation: NA000016804.1 (GSM977028_hg19_wgEncodeCshlShortRnaSeqHmscbmCellTapPlusRawRep1.bigWig),Named Annotation: NA000016805.1 (GSM977028_hg19_wgEncodeCshlShortRnaSeqHmscbmCellTapPlusRawRep2.bigWig)
GSM977028
GSE24565
0.258009
hMSC-BM
Public on Jul 26 2012
Jul 26 2012
9606
CSHL_RnaSeq_hMSC-BM_cell_TAP-Only_shortTotal
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX171103
https://www.ncbi.nlm.nih.gov/biosample/SAMN01095692
1
datatype: RnaSeq,datatype description: Sequencing analysis of RNA expression,rnaextract: shortTotal,rnaextract description: Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation,biorep: 095WC,096WC,095WC,096WC,labexpid: LID48355,LID48356,LID48355,LID48356,labversion: iIDR,readtype: 1x101,readtype description: Single 101 nt reads,replicate: 1,2,localization: cell,localization description: Whole cell,protocol: TAP-Only,protocol description: This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned.,rnaextract: shortTotal,rnaextract description: Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation,biorep: 095WC,096WC,labexpid: LID48355,LID48356,labversion: iIDR,readtype: 1x101,readtype description: Single 101 nt reads
300 Pasteur Dr
Stanford
USA
ENCODE DCC
ENCODE,,DCC
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeCshlShortRnaSeq
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeCshlShortRnaSeq
GSM977029
Illumina HiSeq 2000
May 15 2019
cDNA
transcriptomic
RNA-Seq
total RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX171104,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01095693,Named Annotation: NA000016806.1 (GSM977029_hg19_wgEncodeCshlShortRnaSeqH1neuronsCellTapMinusRawRep1.bigWig),Named Annotation: NA000016807.1 (GSM977029_hg19_wgEncodeCshlShortRnaSeqH1neuronsCellTapMinusRawRep2.bigWig),Named Annotation: NA000016808.1 (GSM977029_hg19_wgEncodeCshlShortRnaSeqH1neuronsCellTapPlusRawRep1.bigWig),Named Annotation: NA000016809.1 (GSM977029_hg19_wgEncodeCshlShortRnaSeqH1neuronsCellTapPlusRawRep2.bigWig)
GSM977029
GSE24565
0.415458
H1-neurons
Public on Jul 26 2012
Jul 26 2012
9606
CSHL_RnaSeq_H1-neurons_cell_TAP-Only_shortTotal
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX171104
https://www.ncbi.nlm.nih.gov/biosample/SAMN01095693
1
datatype: RnaSeq,datatype description: Sequencing analysis of RNA expression,rnaextract: shortTotal,rnaextract description: Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation,biorep: 095WC,096WC,095WC,096WC,labexpid: LID48354,LID48353,LID48354,LID48353,labversion: iIDR,readtype: 1x101,readtype description: Single 101 nt reads,replicate: 1,2,localization: cell,localization description: Whole cell,protocol: CIP-TAP,protocol description: This kind of library was made from RNA < 200 nucleotides that was pre-treated sequentially with Calf Intestinal Alkaline Phosphatase followed by Tobacco Acid Pyrophosphatase. Hence, it will be enriched for capped RNAs.,rnaextract: shortTotal,rnaextract description: Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation,biorep: 095WC,096WC,labexpid: LID48353,LID48354,labversion: iIDR,readtype: 1x101,readtype description: Single 101 nt reads
300 Pasteur Dr
Stanford
USA
ENCODE DCC
ENCODE,,DCC
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeCshlShortRnaSeq
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeCshlShortRnaSeq
GSM977030
Illumina HiSeq 2000
May 15 2019
cDNA
transcriptomic
RNA-Seq
total RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX171105,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01095694,Named Annotation: NA000016810.1 (GSM977030_hg19_wgEncodeCshlShortRnaSeqH1neuronsCellCiptapMinusRawRep1.bigWig),Named Annotation: NA000016811.1 (GSM977030_hg19_wgEncodeCshlShortRnaSeqH1neuronsCellCiptapMinusRawRep2.bigWig),Named Annotation: NA000016812.1 (GSM977030_hg19_wgEncodeCshlShortRnaSeqH1neuronsCellCiptapPlusRawRep1.bigWig),Named Annotation: NA000016813.1 (GSM977030_hg19_wgEncodeCshlShortRnaSeqH1neuronsCellCiptapPlusRawRep2.bigWig)
GSM977030
GSE24565
0.240567
H1-neurons
Public on Jul 26 2012
Jul 26 2012
9606
CSHL_RnaSeq_H1-neurons_cell_CIP-TAP_shortTotal
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX171105
https://www.ncbi.nlm.nih.gov/biosample/SAMN01095694
1
datatype: RnaSeq,datatype description: Sequencing analysis of RNA expression,rnaextract: shortTotal,rnaextract description: Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation,biorep: 095WC,096WC,095WC,096WC,labexpid: LID48357,LID48358,LID48357,LID48358,labversion: iIDR,readtype: 1x101,readtype description: Single 101 nt reads,replicate: 1,2,localization: cell,localization description: Whole cell,protocol: None,protocol description: No special treatment or protocol applies,rnaextract: shortTotal,rnaextract description: Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation,biorep: 095WC,096WC,labexpid: LID48357,LID48358,labversion: iIDR,readtype: 1x101,readtype description: Single 101 nt reads
300 Pasteur Dr
Stanford
USA
ENCODE DCC
ENCODE,,DCC
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeCshlShortRnaSeq
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeCshlShortRnaSeq
GSM977031
Illumina HiSeq 2000
May 15 2019
cDNA
transcriptomic
RNA-Seq
total RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX171106,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01095695,Named Annotation: NA000016814.1 (GSM977031_hg19_wgEncodeCshlShortRnaSeqH1neuronsCellMinusRawRep1.bigWig),Named Annotation: NA000016815.1 (GSM977031_hg19_wgEncodeCshlShortRnaSeqH1neuronsCellMinusRawRep2.bigWig),Named Annotation: NA000016816.1 (GSM977031_hg19_wgEncodeCshlShortRnaSeqH1neuronsCellPlusRawRep1.bigWig),Named Annotation: NA000016817.1 (GSM977031_hg19_wgEncodeCshlShortRnaSeqH1neuronsCellPlusRawRep2.bigWig)
GSM977031
GSE24565
0.640453
H1-neurons
Public on Jul 26 2012
Jul 26 2012
9606
CSHL_RnaSeq_H1-neurons_cell_shortTotal
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX171106
https://www.ncbi.nlm.nih.gov/biosample/SAMN01095695
1
datatype: RnaSeq,datatype description: Sequencing analysis of RNA expression,rnaextract: shortTotal,rnaextract description: Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation,biorep: 091NL,092NL,091NL,092NL,labexpid: LID47654,LID47653,LID47653,LID47654,labversion: iIDR,readtype: 1x101,readtype description: Single 101 nt reads,replicate: 3,4,localization: nucleolus,localization description: The part of the nucleus where ribosomal RNA is actively transcribed,protocol: TAP-Only,protocol description: This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned.,rnaextract: shortTotal,rnaextract description: Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation,biorep: 091NL,092NL,labexpid: LID47653,LID47654,labversion: iIDR,readtype: 1x101,readtype description: Single 101 nt reads
300 Pasteur Dr
Stanford
USA
ENCODE DCC
ENCODE,,DCC
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeCshlShortRnaSeq
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeCshlShortRnaSeq
GSM977032
Illumina HiSeq 2000
May 15 2019
cDNA
transcriptomic
RNA-Seq
nuclear RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX171107,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01095696,Named Annotation: NA000016818.1 (GSM977032_hg19_wgEncodeCshlShortRnaSeqGm12878NucleolusTapMinusRawRep3.bigWig),Named Annotation: NA000016819.1 (GSM977032_hg19_wgEncodeCshlShortRnaSeqGm12878NucleolusTapMinusRawRep4.bigWig),Named Annotation: NA000016820.1 (GSM977032_hg19_wgEncodeCshlShortRnaSeqGm12878NucleolusTapPlusRawRep3.bigWig),Named Annotation: NA000016821.1 (GSM977032_hg19_wgEncodeCshlShortRnaSeqGm12878NucleolusTapPlusRawRep4.bigWig)
GSM977032
GSE24565
0.04087
GM12878
Public on Jul 26 2012
Jul 26 2012
9606
CSHL_RnaSeq_GM12878_nucleolus_TAP-Only_shortTotal
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX171107
https://www.ncbi.nlm.nih.gov/biosample/SAMN01095696
1
datatype: RnaSeq,datatype description: Sequencing analysis of RNA expression,rnaextract: shortTotal,rnaextract description: Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation,biorep: 051WC,052WC,051WC,052WC,labexpid: LID47244,LID47243,LID47244,LID47243,labversion: iIDR,readtype: 1x101,readtype description: Single 101 nt reads,replicate: 1,2,localization description: Whole cell,protocol: TAP-Only,protocol description: This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned.,rnaextract: shortTotal,rnaextract description: Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation,biorep: 051WC,labexpid: LID47243,readtype: 1x101,readtype description: Single 101 nt reads,replicate: 1
300 Pasteur Dr
Stanford
USA
ENCODE DCC
ENCODE,,DCC
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeCshlShortRnaSeq
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeCshlShortRnaSeq
GSM977033
Illumina HiSeq 2000
May 15 2019
cDNA
transcriptomic
RNA-Seq
total RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX171108,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01095697,Named Annotation: NA000016822.1 (GSM977033_hg19_wgEncodeCshlShortRnaSeqHvmf60912033CellShorttotalTapMinusRep1.bigWig),Named Annotation: NA000016823.1 (GSM977033_hg19_wgEncodeCshlShortRnaSeqHvmf60912033CellShorttotalTapPlusRep1.bigWig),Named Annotation: NA000016824.1 (GSM977033_hg19_wgEncodeCshlShortRnaSeqHvmf61004013CellShorttotalTapMinusRep2.bigWig),Named Annotation: NA000016825.1 (GSM977033_hg19_wgEncodeCshlShortRnaSeqHvmf61004013CellShorttotalTapPlusRep2.bigWig)
GSM977033
GSE24565
0.163373
HVMF
Public on Jul 26 2012
Jul 26 2012
9606
CSHL_RnaSeq_HVMF_cell_TAP-Only_shortTotal
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX171108
https://www.ncbi.nlm.nih.gov/biosample/SAMN01095697
1
biomaterial_type: primary cell,cell_type: fibroblast of dermis,donor_id: ENCDO120AAA,ENCDO119AAA,datatype: RnaSeq,datatype description: Sequencing analysis of RNA expression,rnaextract: shortTotal,rnaextract description: Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation,biorep: 050WC,049WC,050WC,049WC,labexpid: LID47241,LID47242,LID47242,LID47241,labversion: iIDR,readtype: 1x101,readtype description: Single 101 nt reads,replicate: 1,2,localization: cell,localization description: Whole cell,protocol: TAP-Only,protocol description: This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned.,rnaextract: shortTotal,rnaextract description: Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation,biorep: 050WC,labexpid: LID47242,readtype: 1x101,readtype description: Single 101 nt reads,replicate: 2
300 Pasteur Dr
Stanford
USA
ENCODE DCC
ENCODE,,DCC
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeCshlShortRnaSeq
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeCshlShortRnaSeq
GSM977034
Illumina HiSeq 2000
May 15 2019
cDNA
transcriptomic
RNA-Seq
total RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX171109,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01095698,Named Annotation: NA000016826.1 (GSM977034_hg19_wgEncodeCshlShortRnaSeqNhdf00608013CellShorttotalTapMinusRep2.bigWig),Named Annotation: NA000016827.1 (GSM977034_hg19_wgEncodeCshlShortRnaSeqNhdf00608013CellShorttotalTapPlusRep2.bigWig),Named Annotation: NA000016828.1 (GSM977034_hg19_wgEncodeCshlShortRnaSeqNhdf70717012CellShorttotalTapMinusRep1.bigWig),Named Annotation: NA000016829.1 (GSM977034_hg19_wgEncodeCshlShortRnaSeqNhdf70717012CellShorttotalTapPlusRep1.bigWig)
GSM977034
GSE24565
0.200127
NHDF
Public on Jul 26 2012
Jul 26 2012
9606
CSHL_RnaSeq_NHDF_cell_TAP-Only_shortTotal
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX171109
https://www.ncbi.nlm.nih.gov/biosample/SAMN01095698
1
datatype: RnaSeq,datatype description: Sequencing analysis of RNA expression,rnaextract: shortTotal,rnaextract description: Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation,biorep: 055WC,056WC,056WC,055WC,labexpid: LID47434,LID47433,LID47434,LID47433,labversion: iIDR,readtype: 1x101,readtype description: Single 101 nt reads,replicate: 1,2,localization: cell,localization description: Whole cell,protocol: TAP-Only,protocol description: This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned.,rnaextract: shortTotal,rnaextract description: Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation,biorep: 056WC,labexpid: LID47434,readtype: 1x101,readtype description: Single 101 nt reads,replicate: 2
300 Pasteur Dr
Stanford
USA
ENCODE DCC
ENCODE,,DCC
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeCshlShortRnaSeq
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeCshlShortRnaSeq
GSM977035
Illumina HiSeq 2000
May 15 2019
cDNA
transcriptomic
RNA-Seq
total RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX171110,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01095699,Named Annotation: NA000016830.1 (GSM977035_hg19_wgEncodeCshlShortRnaSeqHaoaf609010111CellTapMinusRep2.bigWig),Named Annotation: NA000016831.1 (GSM977035_hg19_wgEncodeCshlShortRnaSeqHaoaf609010111CellTapPlusRep2.bigWig),Named Annotation: NA000016832.1 (GSM977035_hg19_wgEncodeCshlShortRnaSeqHaoaf61113019CellTapMinusRep1.bigWig),Named Annotation: NA000016833.1 (GSM977035_hg19_wgEncodeCshlShortRnaSeqHaoaf61113019CellTapPlusRep1.bigWig)
GSM977035
GSE24565
0.030855
HAoAF
Public on Jul 26 2012
Jul 26 2012
9606
CSHL_RnaSeq_HAoAF_cell_TAP-Only_shortTotal
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX171110
https://www.ncbi.nlm.nih.gov/biosample/SAMN01095699
1
biomaterial_type: primary cell,cell_type: osteoblast,donor_id: ENCDO123AAA,ENCDO124AAA,datatype: RnaSeq,datatype description: Sequencing analysis of RNA expression,rnaextract: shortTotal,rnaextract description: Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation,biorep: 053WC,054WC,054WC,053WC,labexpid: LID47431,LID47431,LID47432,LID47432,labversion: iIDR,readtype: 1x101,readtype description: Single 101 nt reads,replicate: 1,2,localization: cell,localization description: Whole cell,protocol: TAP-Only,protocol description: This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned.,rnaextract: shortTotal,rnaextract description: Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation,biorep: 054WC,labexpid: LID47432,readtype: 1x101,readtype description: Single 101 nt reads,replicate: 2
300 Pasteur Dr
Stanford
USA
ENCODE DCC
ENCODE,,DCC
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeCshlShortRnaSeq
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeCshlShortRnaSeq
GSM977036
Illumina HiSeq 2000
May 15 2019
cDNA
transcriptomic
RNA-Seq
total RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX171111,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01095700,Named Annotation: NA000016834.1 (GSM977036_hg19_wgEncodeCshlShortRnaSeqHob00902021CellShorttotalTapMinusRep2.bigWig),Named Annotation: NA000016835.1 (GSM977036_hg19_wgEncodeCshlShortRnaSeqHob00902021CellShorttotalTapPlusRep2.bigWig),Named Annotation: NA000016836.1 (GSM977036_hg19_wgEncodeCshlShortRnaSeqHobCellTapMinusRawRep1.bigWig),Named Annotation: NA000016837.1 (GSM977036_hg19_wgEncodeCshlShortRnaSeqHobCellTapPlusRawRep1.bigWig)
GSM977036
GSE24565
0
HOB
Public on Jul 26 2012
Jul 26 2012
9606
CSHL_RnaSeq_HOB_cell_TAP-Only_shortTotal
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX171111
https://www.ncbi.nlm.nih.gov/biosample/SAMN01095700
1
datatype: RnaSeq,datatype description: Sequencing analysis of RNA expression,rnaextract: shortTotal,rnaextract description: Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation,biorep: 059WC,059WC,060WC,060WC,labexpid: LID47475,LID47475,LID47476,LID47476,labversion: iIDR,readtype: 1x101,readtype description: Single 101 nt reads,replicate: 1,2,localization: cell,localization description: Whole cell,protocol: TAP-Only,protocol description: This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned.,rnaextract: shortTotal,rnaextract description: Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation,biorep: 059WC,labexpid: LID47475,readtype: 1x101,readtype description: Single 101 nt reads,replicate: 1
300 Pasteur Dr
Stanford
USA
ENCODE DCC
ENCODE,,DCC
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeCshlShortRnaSeq
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeCshlShortRnaSeq
GSM977037
Illumina HiSeq 2000
May 15 2019
cDNA
transcriptomic
RNA-Seq
total RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX171112,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01095701,Named Annotation: NA000016838.1 (GSM977037_hg19_wgEncodeCshlShortRnaSeqHch00113082pCellShorttotalTapMinusRep1.bigWig),Named Annotation: NA000016839.1 (GSM977037_hg19_wgEncodeCshlShortRnaSeqHch00113082pCellShorttotalTapPlusRep1.bigWig),Named Annotation: NA000016840.1 (GSM977037_hg19_wgEncodeCshlShortRnaSeqHch81008082CellShorttotalTapMinusRep2.bigWig),Named Annotation: NA000016841.1 (GSM977037_hg19_wgEncodeCshlShortRnaSeqHch81008082CellShorttotalTapPlusRep2.bigWig)
GSM977037
GSE24565
0.260659
HCH
Public on Jul 26 2012
Jul 26 2012
9606
CSHL_RnaSeq_HCH_cell_TAP-Only_shortTotal
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX171112
https://www.ncbi.nlm.nih.gov/biosample/SAMN01095701
1
datatype: RnaSeq,datatype description: Sequencing analysis of RNA expression,rnaextract: shortTotal,rnaextract description: Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation,biorep: 061WC,062WC,062WC,061WC,labexpid: LID47478,LID47477,LID47478,LID47477,labversion: iIDR,readtype: 1x101,readtype description: Single 101 nt reads,replicate: 1,2,localization: cell,localization description: Whole cell,protocol: TAP-Only,protocol description: This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned.,rnaextract: shortTotal,rnaextract description: Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation,biorep: 062WC,labexpid: LID47478,readtype: 1x101,readtype description: Single 101 nt reads,replicate: 2
300 Pasteur Dr
Stanford
USA
ENCODE DCC
ENCODE,,DCC
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeCshlShortRnaSeq
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeCshlShortRnaSeq
GSM977038
Illumina HiSeq 2000
May 15 2019
cDNA
transcriptomic
RNA-Seq
total RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX171113,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01095702,Named Annotation: NA000016842.1 (GSM977038_hg19_wgEncodeCshlShortRnaSeqHfdpc01005032CellTapMinusRep2.bigWig),Named Annotation: NA000016843.1 (GSM977038_hg19_wgEncodeCshlShortRnaSeqHfdpc01005032CellTapPlusRep2.bigWig),Named Annotation: NA000016844.1 (GSM977038_hg19_wgEncodeCshlShortRnaSeqHfdpc01027033CellTapMinusRep1.bigWig),Named Annotation: NA000016845.1 (GSM977038_hg19_wgEncodeCshlShortRnaSeqHfdpc01027033CellTapPlusRep1.bigWig)
GSM977038
GSE24565
0.255124
HFDPC
Public on Jul 26 2012
Jul 26 2012
9606
CSHL_RnaSeq_HFDPC_cell_TAP-Only_shortTotal
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX171113
https://www.ncbi.nlm.nih.gov/biosample/SAMN01095702
1
datatype: RnaSeq,datatype description: Sequencing analysis of RNA expression,rnaextract: shortTotal,rnaextract description: Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation,biorep: 047WC,048WC,047WC,048WC,labexpid: LID47239,LID47240,LID47239,LID47240,labversion: iIDR,readtype: 1x101,readtype description: Single 101 nt reads,replicate: 1,2,localization: cell,localization description: Whole cell,protocol: TAP-Only,protocol description: This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned.,rnaextract: shortTotal,rnaextract description: Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation,biorep: 048WC,labexpid: LID47240,readtype: 1x101,readtype description: Single 101 nt reads,replicate: 2
300 Pasteur Dr
Stanford
USA
ENCODE DCC
ENCODE,,DCC
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeCshlShortRnaSeq
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeCshlShortRnaSeq
GSM977039
Illumina HiSeq 2000
May 15 2019
cDNA
transcriptomic
RNA-Seq
total RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX171114,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01095703,Named Annotation: NA000016846.1 (GSM977039_hg19_wgEncodeCshlShortRnaSeqSkmc812190217CellTapMinusRep2.bigWig),Named Annotation: NA000016847.1 (GSM977039_hg19_wgEncodeCshlShortRnaSeqSkmc812190217CellTapPlusRep2.bigWig),Named Annotation: NA000016848.1 (GSM977039_hg19_wgEncodeCshlShortRnaSeqSkmc9011302CellShorttotalTapMinusRep1.bigWig),Named Annotation: NA000016849.1 (GSM977039_hg19_wgEncodeCshlShortRnaSeqSkmc9011302CellShorttotalTapPlusRep1.bigWig)
GSM977039
GSE24565
0.083869
SkMC
Public on Jul 26 2012
Jul 26 2012
9606
CSHL_RnaSeq_SkMC_cell_TAP-Only_shortTotal
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX171114
https://www.ncbi.nlm.nih.gov/biosample/SAMN01095703
1
datatype: RnaSeq,datatype description: Sequencing analysis of RNA expression,rnaextract: shortTotal,rnaextract description: Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation,biorep: 058WC,057WC,057WC,058WC,labexpid: LID47435,LID47436,LID47435,LID47436,labversion: iIDR,readtype: 1x101,readtype description: Single 101 nt reads,replicate: 1,2,localization: cell,localization description: Whole cell,protocol: TAP-Only,protocol description: This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned.,rnaextract: shortTotal,rnaextract description: Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation,biorep: 057WC,labexpid: LID47435,readtype: 1x101,readtype description: Single 101 nt reads,replicate: 1
300 Pasteur Dr
Stanford
USA
ENCODE DCC
ENCODE,,DCC
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeCshlShortRnaSeq
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeCshlShortRnaSeq
GSM977040
Illumina HiSeq 2000
May 15 2019
cDNA
transcriptomic
RNA-Seq
total RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX171115,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01095704,Named Annotation: NA000016850.1 (GSM977040_hg19_wgEncodeCshlShortRnaSeqHaoec70717061CellTapMinusRep1.bigWig),Named Annotation: NA000016851.1 (GSM977040_hg19_wgEncodeCshlShortRnaSeqHaoec70717061CellTapPlusRep1.bigWig),Named Annotation: NA000016852.1 (GSM977040_hg19_wgEncodeCshlShortRnaSeqHaoec80611021CellTapMinusRep2.bigWig),Named Annotation: NA000016853.1 (GSM977040_hg19_wgEncodeCshlShortRnaSeqHaoec80611021CellTapPlusRep2.bigWig)
GSM977040
GSE24565
0.22803
HAoEC
Public on Jul 26 2012
Jul 26 2012
9606
CSHL_RnaSeq_HAoEC_cell_TAP-Only_shortTotal
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX171115
https://www.ncbi.nlm.nih.gov/biosample/SAMN01095704
1
datatype: RnaSeq,datatype description: Sequencing analysis of RNA expression,rnaextract: shortTotal,rnaextract description: Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation,biorep: 065WC,065WC,066WC,066WC,labexpid: LID47479,LID47479,LID47480,LID47480,labversion: iIDR,readtype: 1x101,readtype description: Single 101 nt reads,replicate: 1,2,localization: cell,localization description: Whole cell,protocol: TAP-Only,protocol description: This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned.,rnaextract: shortTotal,rnaextract description: Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation,biorep: 065WC,labexpid: LID47479,readtype: 1x101,readtype description: Single 101 nt reads,replicate: 1
300 Pasteur Dr
Stanford
USA
ENCODE DCC
ENCODE,,DCC
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeCshlShortRnaSeq
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeCshlShortRnaSeq
GSM977041
Illumina HiSeq 2000
May 15 2019
cDNA
transcriptomic
RNA-Seq
total RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX171116,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01095705,Named Annotation: NA000016854.1 (GSM977041_hg19_wgEncodeCshlShortRnaSeqHmscat010260412CellTapMinusRep1.bigWig),Named Annotation: NA000016855.1 (GSM977041_hg19_wgEncodeCshlShortRnaSeqHmscat010260412CellTapPlusRep1.bigWig),Named Annotation: NA000016856.1 (GSM977041_hg19_wgEncodeCshlShortRnaSeqHmscat906160112CellTapMinusRep2.bigWig),Named Annotation: NA000016857.1 (GSM977041_hg19_wgEncodeCshlShortRnaSeqHmscat906160112CellTapPlusRep2.bigWig)
GSM977041
GSE24565
0.261689
hMSC-AT
Public on Jul 26 2012
Jul 26 2012
9606
CSHL_RnaSeq_hMSC-AT_cell_TAP-Only_shortTotal
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX171116
https://www.ncbi.nlm.nih.gov/biosample/SAMN01095705
1
datatype: RnaSeq,datatype description: Sequencing analysis of RNA expression,rnaextract: shortTotal,rnaextract description: Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation,biorep: 091CH,091CH,092CH,092CH,labexpid: LID47655,LID47656,LID47655,LID47656,labversion: iIDR,readtype: 1x101,readtype description: Single 101 nt reads,replicate: 3,4,localization: chromatin,localization description: Nuclear DNA and associated proteins,protocol: TAP-Only,protocol description: This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned.,rnaextract: shortTotal,rnaextract description: Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation,biorep: 091CH,092CH,labexpid: LID47655,LID47656,labversion: iIDR,readtype: 1x101,readtype description: Single 101 nt reads
300 Pasteur Dr
Stanford
USA
ENCODE DCC
ENCODE,,DCC
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeCshlShortRnaSeq
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeCshlShortRnaSeq
GSM977042
Illumina HiSeq 2000
May 15 2019
cDNA
transcriptomic
RNA-Seq
nuclear RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX171117,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01095706,Named Annotation: NA000016858.1 (GSM977042_hg19_wgEncodeCshlShortRnaSeqGm12878ChromatinTapMinusRep3.bigWig),Named Annotation: NA000016859.1 (GSM977042_hg19_wgEncodeCshlShortRnaSeqGm12878ChromatinTapMinusRep4.bigWig),Named Annotation: NA000016860.1 (GSM977042_hg19_wgEncodeCshlShortRnaSeqGm12878ChromatinTapPlusRep3.bigWig),Named Annotation: NA000016861.1 (GSM977042_hg19_wgEncodeCshlShortRnaSeqGm12878ChromatinTapPlusRep4.bigWig)
GSM977042
GSE24565
0.057964
GM12878
Public on Jul 26 2012
Jul 26 2012
9606
CSHL_RnaSeq_GM12878_chromatin_TAP-Only_shortTotal
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX171117
https://www.ncbi.nlm.nih.gov/biosample/SAMN01095706
1
datatype: RnaSeq,datatype description: Sequencing analysis of RNA expression,rnaextract: shortTotal,rnaextract description: Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation,biorep: 081WC,081WC,082WC,082WC,labexpid: LID47611,LID47612,LID47611,LID47612,labversion: iIDR,readtype: 1x101,readtype description: Single 101 nt reads,replicate: 1,2,localization: cell,localization description: Whole cell,protocol: TAP-Only,protocol description: This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned.,rnaextract: shortTotal,rnaextract description: Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation,biorep: 081WC,082WC,labexpid: LID47611,LID47612,labversion: iIDR,readtype: 1x101,readtype description: Single 101 nt reads
300 Pasteur Dr
Stanford
USA
ENCODE DCC
ENCODE,,DCC
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeCshlShortRnaSeq
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeCshlShortRnaSeq
GSM977045
Illumina HiSeq 2000
May 15 2019
cDNA
transcriptomic
RNA-Seq
total RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX171120,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01095709,Named Annotation: NA000016870.1 (GSM977045_hg19_wgEncodeCshlShortRnaSeqNhemfm2CellTapMinusRep1.bigWig),Named Annotation: NA000016871.1 (GSM977045_hg19_wgEncodeCshlShortRnaSeqNhemfm2CellTapMinusRep2.bigWig),Named Annotation: NA000016872.1 (GSM977045_hg19_wgEncodeCshlShortRnaSeqNhemfm2CellTapPlusRep1.bigWig),Named Annotation: NA000016873.1 (GSM977045_hg19_wgEncodeCshlShortRnaSeqNhemfm2CellTapPlusRep2.bigWig)
GSM977045
GSE24565
0.179791
NHEM.f_M2
Public on Jul 26 2012
Jul 26 2012
9606
CSHL_RnaSeq_NHEM.f_M2_cell_TAP-Only_shortTotal
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX171120
https://www.ncbi.nlm.nih.gov/biosample/SAMN01095709
1
datatype: RnaSeq,datatype description: Sequencing analysis of RNA expression,rnaextract: shortTotal,rnaextract description: Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation,biorep: 079WC,080WC,079WC,080WC,labexpid: LID47610,LID47609,LID47610,LID47609,labversion: iIDR,readtype: 1x101,readtype description: Single 101 nt reads,replicate: 1,2,localization: cell,localization description: Whole cell,protocol: TAP-Only,protocol description: This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned.,rnaextract: shortTotal,rnaextract description: Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation,biorep: 079WC,080WC,labexpid: LID47609,LID47610,labversion: iIDR,readtype: 1x101,readtype description: Single 101 nt reads
300 Pasteur Dr
Stanford
USA
ENCODE DCC
ENCODE,,DCC
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeCshlShortRnaSeq
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeCshlShortRnaSeq
GSM977046
Illumina HiSeq 2000
May 15 2019
cDNA
transcriptomic
RNA-Seq
total RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX171121,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01095710,Named Annotation: NA000016874.1 (GSM977046_hg19_wgEncodeCshlShortRnaSeqHwpCellTapMinusRep1.bigWig),Named Annotation: NA000016875.1 (GSM977046_hg19_wgEncodeCshlShortRnaSeqHwpCellTapMinusRep2.bigWig),Named Annotation: NA000016876.1 (GSM977046_hg19_wgEncodeCshlShortRnaSeqHwpCellTapPlusRep1.bigWig),Named Annotation: NA000016877.1 (GSM977046_hg19_wgEncodeCshlShortRnaSeqHwpCellTapPlusRep2.bigWig)
GSM977046
GSE24565
0.159667
HWP
Public on Jul 26 2012
Jul 26 2012
9606
CSHL_RnaSeq_HWP_cell_TAP-Only_shortTotal
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX171121
https://www.ncbi.nlm.nih.gov/biosample/SAMN01095710
1
datatype: RnaSeq,datatype description: Sequencing analysis of RNA expression,rnaextract: shortTotal,rnaextract description: Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation,biorep: 083WC,083WC,084WC,084WC,labexpid: LID47613,LID47614,LID47613,LID47614,labversion: iIDR,readtype: 1x101,readtype description: Single 101 nt reads,replicate: 1,2,localization: cell,localization description: Whole cell,protocol: TAP-Only,protocol description: This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned.,rnaextract: shortTotal,rnaextract description: Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation,biorep: 083WC,084WC,labexpid: LID47613,LID47614,labversion: iIDR,readtype: 1x101,readtype description: Single 101 nt reads
300 Pasteur Dr
Stanford
USA
ENCODE DCC
ENCODE,,DCC
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeCshlShortRnaSeq
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeCshlShortRnaSeq
GSM977047
Illumina HiSeq 2000
May 15 2019
cDNA
transcriptomic
RNA-Seq
total RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX171122,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01095711,Named Annotation: NA000016878.1 (GSM977047_hg19_wgEncodeCshlShortRnaSeqNhemm2CellTapMinusRep1.bigWig),Named Annotation: NA000016879.1 (GSM977047_hg19_wgEncodeCshlShortRnaSeqNhemm2CellTapMinusRep2.bigWig),Named Annotation: NA000016880.1 (GSM977047_hg19_wgEncodeCshlShortRnaSeqNhemm2CellTapPlusRep1.bigWig),Named Annotation: NA000016881.1 (GSM977047_hg19_wgEncodeCshlShortRnaSeqNhemm2CellTapPlusRep2.bigWig)
GSM977047
GSE24565
0.004471
NHEM_M2
Public on Jul 26 2012
Jul 26 2012
9606
CSHL_RnaSeq_NHEM_M2_cell_TAP-Only_shortTotal
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX171122
https://www.ncbi.nlm.nih.gov/biosample/SAMN01095711
1
datatype: RnaSeq,datatype description: Sequencing analysis of RNA expression,rnaextract: shortTotal,rnaextract description: Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation,biorep: 069WC,069WC,070WC,070WC,labexpid: LID47515,LID47516,LID47516,LID47515,labversion: iIDR,readtype: 1x101,readtype description: Single 101 nt reads,replicate: 1,2,localization: cell,localization description: Whole cell,protocol: TAP-Only,protocol description: This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned.,rnaextract: shortTotal,rnaextract description: Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation,biorep: 069WC,070WC,labexpid: LID47515,LID47516,labversion: iIDR,readtype: 1x101,readtype description: Single 101 nt reads
300 Pasteur Dr
Stanford
USA
ENCODE DCC
ENCODE,,DCC
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeCshlShortRnaSeq
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeCshlShortRnaSeq
GSM977048
Illumina HiSeq 2000
May 15 2019
cDNA
transcriptomic
RNA-Seq
total RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX171123,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01095712,Named Annotation: NA000016882.1 (GSM977048_hg19_wgEncodeCshlShortRnaSeqHmscucCellTapMinusRep1.bigWig),Named Annotation: NA000016883.1 (GSM977048_hg19_wgEncodeCshlShortRnaSeqHmscucCellTapMinusRep2.bigWig),Named Annotation: NA000016884.1 (GSM977048_hg19_wgEncodeCshlShortRnaSeqHmscucCellTapPlusRep1.bigWig),Named Annotation: NA000016885.1 (GSM977048_hg19_wgEncodeCshlShortRnaSeqHmscucCellTapPlusRep2.bigWig)
GSM977048
GSE24565
0.147092
hMSC-UC
Public on Jul 26 2012
Jul 26 2012
9606
CSHL_RnaSeq_hMSC-UC_cell_TAP-Only_shortTotal
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX171123
https://www.ncbi.nlm.nih.gov/biosample/SAMN01095712
1
datatype: RnaSeq,datatype description: Sequencing analysis of RNA expression,rnaextract: shortTotal,rnaextract description: Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation,biorep: 071WC,072WC,072WC,071WC,labexpid: LID47518,LID47517,LID47518,LID47517,labversion: iIDR,readtype: 1x101,readtype description: Single 101 nt reads,replicate: 1,2,localization: cell,localization description: Whole cell,protocol: TAP-Only,protocol description: This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned.,rnaextract: shortTotal,rnaextract description: Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation,biorep: 071WC,072WC,labexpid: LID47517,LID47518,labversion: iIDR,readtype: 1x101,readtype description: Single 101 nt reads
300 Pasteur Dr
Stanford
USA
ENCODE DCC
ENCODE,,DCC
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeCshlShortRnaSeq
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeCshlShortRnaSeq
GSM977049
Illumina HiSeq 2000
May 15 2019
cDNA
transcriptomic
RNA-Seq
total RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX171124,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01095713,Named Annotation: NA000016886.1 (GSM977049_hg19_wgEncodeCshlShortRnaSeqHpcplCellTapMinusRep1.bigWig),Named Annotation: NA000016887.1 (GSM977049_hg19_wgEncodeCshlShortRnaSeqHpcplCellTapMinusRep2.bigWig),Named Annotation: NA000016888.1 (GSM977049_hg19_wgEncodeCshlShortRnaSeqHpcplCellTapPlusRep1.bigWig),Named Annotation: NA000016889.1 (GSM977049_hg19_wgEncodeCshlShortRnaSeqHpcplCellTapPlusRep2.bigWig)
GSM977049
GSE24565
0.061576
HPC-PL
Public on Jul 26 2012
Jul 26 2012
9606
CSHL_RnaSeq_HPC-PL_cell_TAP-Only_shortTotal
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX171124
https://www.ncbi.nlm.nih.gov/biosample/SAMN01095713
1
biomaterial_type: primary cell,cell_type: mammary epithelial cell,donor_id: ENCDO131AAA,datatype: RnaSeq,datatype description: Sequencing analysis of RNA expression,rnaextract: shortTotal,rnaextract description: Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation,biorep: 063WC,labexpid: LID47657,labversion: iIDR,readtype: 1x101,readtype description: Single 101 nt reads,replicate: 1,localization: cell,localization description: Whole cell,protocol: TAP-Only,protocol description: This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned.,rnaextract: shortTotal,rnaextract description: Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation,biorep: 063WC,labexpid: LID47657,labversion: iIDR,readtype: 1x101,readtype description: Single 101 nt reads
300 Pasteur Dr
Stanford
USA
ENCODE DCC
ENCODE,,DCC
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeCshlShortRnaSeq
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeCshlShortRnaSeq
GSM977050
Illumina HiSeq 2000
May 15 2019
cDNA
transcriptomic
RNA-Seq
total RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX171125,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01095714,Named Annotation: NA000016890.1 (GSM977050_hg19_wgEncodeCshlShortRnaSeqHmepcCellTapMinusRep1.bigWig),Named Annotation: NA000016891.1 (GSM977050_hg19_wgEncodeCshlShortRnaSeqHmepcCellTapPlusRep1.bigWig)
GSM977050
GSE24565
0.31571
HMEpC
Public on Jul 26 2012
Jul 26 2012
9606
CSHL_RnaSeq_HMEpC_cell_TAP-Only_shortTotal
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX171125
https://www.ncbi.nlm.nih.gov/biosample/SAMN01095714
1
datatype: RnaSeq,datatype description: Sequencing analysis of RNA expression,rnaextract: shortTotal,rnaextract description: Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation,biorep: 094WC,093WC,093WC,094WC,labexpid: LID47615,LID47615,LID47616,LID47616,labversion: iIDR,readtype: 1x101,readtype description: Single 101 nt reads,replicate: 1,2,localization: cell,localization description: Whole cell,protocol: TAP-Only,protocol description: This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned.,rnaextract: shortTotal,rnaextract description: Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation,biorep: 093WC,094WC,labexpid: LID47615,LID47616,labversion: iIDR,readtype: 1x101,readtype description: Single 101 nt reads
300 Pasteur Dr
Stanford
USA
ENCODE DCC
ENCODE,,DCC
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeCshlShortRnaSeq
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeCshlShortRnaSeq
GSM977051
Illumina HiSeq 2000
May 15 2019
cDNA
transcriptomic
RNA-Seq
total RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX171126,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01095715,Named Annotation: NA000016892.1 (GSM977051_hg19_wgEncodeCshlShortRnaSeqHsavecCellTapMinusRep1.bigWig),Named Annotation: NA000016893.1 (GSM977051_hg19_wgEncodeCshlShortRnaSeqHsavecCellTapMinusRep2.bigWig),Named Annotation: NA000016894.1 (GSM977051_hg19_wgEncodeCshlShortRnaSeqHsavecCellTapPlusRep1.bigWig),Named Annotation: NA000016895.1 (GSM977051_hg19_wgEncodeCshlShortRnaSeqHsavecCellTapPlusRep2.bigWig)
GSM977051
GSE24565
0.183631
HSaVEC
Public on Jul 26 2012
Jul 26 2012
9606
CSHL_RnaSeq_HSaVEC_cell_TAP-Only_shortTotal
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX171126
https://www.ncbi.nlm.nih.gov/biosample/SAMN01095715
1
datatype: RnaSeq,datatype description: Sequencing analysis of RNA expression,rnaextract: shortTotal,rnaextract description: Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation,biorep: 073WC,074WC,073WC,074WC,labexpid: LID47520,LID47519,LID47519,LID47520,labversion: iIDR,readtype: 1x101,readtype description: Single 101 nt reads,replicate: 1,2,localization: cell,localization description: Whole cell,protocol: TAP-Only,protocol description: This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned.,rnaextract: shortTotal,rnaextract description: Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation,biorep: 073WC,074WC,labexpid: LID47519,LID47520,labversion: iIDR,readtype: 1x101,readtype description: Single 101 nt reads
300 Pasteur Dr
Stanford
USA
ENCODE DCC
ENCODE,,DCC
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeCshlShortRnaSeq
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeCshlShortRnaSeq
GSM977052
Illumina HiSeq 2000
May 15 2019
cDNA
transcriptomic
RNA-Seq
total RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX171127,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01095716,Named Annotation: NA000016896.1 (GSM977052_hg19_wgEncodeCshlShortRnaSeqHpiepcCellTapMinusRep1.bigWig),Named Annotation: NA000016897.1 (GSM977052_hg19_wgEncodeCshlShortRnaSeqHpiepcCellTapMinusRep2.bigWig),Named Annotation: NA000016898.1 (GSM977052_hg19_wgEncodeCshlShortRnaSeqHpiepcCellTapPlusRep1.bigWig),Named Annotation: NA000016899.1 (GSM977052_hg19_wgEncodeCshlShortRnaSeqHpiepcCellTapPlusRep2.bigWig)
GSM977052
GSE24565
0.067932
HPIEpC
Public on Jul 26 2012
Jul 26 2012
9606
CSHL_RnaSeq_HPIEpC_cell_TAP-Only_shortTotal
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX171127
https://www.ncbi.nlm.nih.gov/biosample/SAMN01095716
1
cell line: FlpIn T-Rex Human embryonic kidney 293 stable cell line,photoactivatable ribonucleoside and crosslinking wavelength: 4-SU / 365 nm,antibody: anti-FLAG M2 [Sigma-Aldrich, cat# F1804, lot#101M6216],immunoprecipitated protein: wt FLAG-HA FMR1 iso1
1230 York Avenue Box 186
New York
USA
The Rockefeller University
Manuel,,Ascano, Jr.
Fastq was converted to fasta using FASTX Toolkit 0.0.13: fastq_to_fasta -v,Adapters were removed using FASTX Toolkit: fastx_clipper -v -a TCGTATGCCGTCTTCTGCTTG -l 13,Reads were mapped to hg19 using bowtie version 0.12.7: bowtie bowtie/base/hg19 -v 2 -m 10 --all --best --strata,Sites were determined using PARalyzer v1.1,Genome_build: hg19,Supplementary_files_format_and_content: bed files reporting target sites for RNA-binding proteins
Cell pellets were lysed in NP40 lysis buffer, centrifuged, and the resulting supernatants used in subsequent steps. The cleared supernatants were incubated with Rnase T1 (Fermentas) at 22ºC, for 15 min, then cooled on ice. FLAG-antibody conjugate paramagnetic beads (Dynabeads, Invitrogen) were added to each supernatant to begin immunoprecipitation. Immunoprecipitates were subjected to dephosphorylation using calf-intestinal alkaline phosphatase (NEB), followed by three buffer washes, then treatment with T4 polynucleotide kinase (NEB) using gamma radiolabelled - 32P ATP. Radiolaballed immunoprecipitates were then fractionated by SDS-PAGE. The immunoprecipitated bands of interest were excised, electroeluted, and treated with Proteinase K to isolate crosslinked RNAs. Crosslinked RNAs were taken through a standard adapter-mediated small RNA cloning protocol and sequenced using Illumina GAII platform (or HiSeq).
GSM977615
Illumina HiSeq 2000
May 15 2019
other
transcriptomic
RNA-Seq
total RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX171147,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01095728
GSM977615
GSE39682,GSE39686
0.124271
FlpIn T-Rex Human embryonic kidney 293 stable cell line
Public on Dec 13 2012
Jul 26 2012
9606
wt FLAG-HA FMR1 iso1
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX171147
https://www.ncbi.nlm.nih.gov/biosample/SAMN01095728
1
cell line: FlpIn T-Rex Human embryonic kidney 293 stable cell line,photoactivatable ribonucleoside and crosslinking wavelength: 4-SU / 365 nm,antibody: anti-FLAG M2 [Sigma-Aldrich, cat# F1804, lot#101M6216],immunoprecipitated protein: wt FLAG-HA FMR1 iso7
1230 York Avenue Box 186
New York
USA
The Rockefeller University
Manuel,,Ascano, Jr.
Fastq was converted to fasta using FASTX Toolkit 0.0.13: fastq_to_fasta -v,Adapters were removed using FASTX Toolkit: fastx_clipper -v -a TCGTATGCCGTCTTCTGCTTG -l 13,Reads were mapped to hg19 using bowtie version 0.12.7: bowtie bowtie/base/hg19 -v 2 -m 10 --all --best --strata,Sites were determined using PARalyzer v1.1,Genome_build: hg19,Supplementary_files_format_and_content: bed files reporting target sites for RNA-binding proteins
Cell pellets were lysed in NP40 lysis buffer, centrifuged, and the resulting supernatants used in subsequent steps. The cleared supernatants were incubated with Rnase T1 (Fermentas) at 22ºC, for 15 min, then cooled on ice. FLAG-antibody conjugate paramagnetic beads (Dynabeads, Invitrogen) were added to each supernatant to begin immunoprecipitation. Immunoprecipitates were subjected to dephosphorylation using calf-intestinal alkaline phosphatase (NEB), followed by three buffer washes, then treatment with T4 polynucleotide kinase (NEB) using gamma radiolabelled - 32P ATP. Radiolaballed immunoprecipitates were then fractionated by SDS-PAGE. The immunoprecipitated bands of interest were excised, electroeluted, and treated with Proteinase K to isolate crosslinked RNAs. Crosslinked RNAs were taken through a standard adapter-mediated small RNA cloning protocol and sequenced using Illumina GAII platform (or HiSeq).
GSM977616
Illumina HiSeq 2000
May 15 2019
other
transcriptomic
RNA-Seq
total RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX171148,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01095729
GSM977616
GSE39682,GSE39686
0
FlpIn T-Rex Human embryonic kidney 293 stable cell line
Public on Dec 13 2012
Jul 26 2012
9606
wt FLAG-HA FMR1 iso7
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX171148
https://www.ncbi.nlm.nih.gov/biosample/SAMN01095729
1
sample type: Cytoplasm,antibody: Input,cell line: HeLa,sample fraction: extract
7-9, Quai Saint Bernard
Paris
France
IBPS - Institut Biologie Paris Seine
Eric,,Batsche
Sequences were aligned to the genome (GRCh37) using oligomap (Berninger, P., Gaidatzis, D., van Nimwegen, E. & Zavolan, M. 2008. Computational analysis of small RNA cloning data. Methods 44, 13-21) to find alignments with up to 1 error (replacement, insertion, or deletion). Alignments were filtered to include only the best matches for each sequence. Sequences with >5 alignments were filtered out.,BED tracks were calculated. For each reads their number were indicated followed by an underscore and the length (in nucleotide) of the considered read. Number of clones of the same sequence is indicated in the score label of the BED tracks. sRNAs bound to AGO2 appear in red, sRNAs bound to the control IgG are in blue, and Input are in black.,Genome_build: GRCh37 / hg19,Supplementary_files_format_and_content: BED tracks were calculated. For each reads their number were indicated followed by an underscore and the length (in nucleotide) of the considered read. Number of clones of the same sequence is indicated in the score label of the BED tracks. sRNAs bound to
Following digestion with DNase (RNase free), short RNAs below 100 bp were gel-purified, poly(A)-tailed using poly(A) polymerase, treated with tobacco acid pyrophosphastase, and RNA adapters were ligated to the 5’phosphate of the RNA. cDNA was synthesized and PCR-amplified.
GSM978497
Illumina HiSeq 2000
May 15 2019
cDNA
transcriptomic
RNA-Seq
total RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX171597,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01096075
GSM978497
GSE39748,GSE39749
0.052389
HeLa cells (ATCC)
Public on Aug 22 2012
Jul 30 2012
9606
EC-input
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX171597
https://www.ncbi.nlm.nih.gov/biosample/SAMN01096075
1
sample type: Cytoplasm,antibody: IgG,cell line: HeLa,sample fraction: immunoprecipitation
7-9, Quai Saint Bernard
Paris
France
IBPS - Institut Biologie Paris Seine
Eric,,Batsche
Sequences were aligned to the genome (GRCh37) using oligomap (Berninger, P., Gaidatzis, D., van Nimwegen, E. & Zavolan, M. 2008. Computational analysis of small RNA cloning data. Methods 44, 13-21) to find alignments with up to 1 error (replacement, insertion, or deletion). Alignments were filtered to include only the best matches for each sequence. Sequences with >5 alignments were filtered out.,BED tracks were calculated. For each reads their number were indicated followed by an underscore and the length (in nucleotide) of the considered read. Number of clones of the same sequence is indicated in the score label of the BED tracks. sRNAs bound to AGO2 appear in red, sRNAs bound to the control IgG are in blue, and Input are in black.,Genome_build: GRCh37 / hg19,Supplementary_files_format_and_content: BED tracks were calculated. For each reads their number were indicated followed by an underscore and the length (in nucleotide) of the considered read. Number of clones of the same sequence is indicated in the score label of the BED tracks. sRNAs bound to
Following digestion with DNase (RNase free), short RNAs below 100 bp were gel-purified, poly(A)-tailed using poly(A) polymerase, treated with tobacco acid pyrophosphastase, and RNA adapters were ligated to the 5’phosphate of the RNA. cDNA was synthesized and PCR-amplified.
GSM978498
Illumina HiSeq 2000
May 15 2019
cDNA
transcriptomic
RNA-Seq
total RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX171598,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01096076
GSM978498
GSE39748,GSE39749
0.263002
HeLa cells (ATCC)
Public on Aug 22 2012
Jul 30 2012
9606
EC-IgG
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX171598
https://www.ncbi.nlm.nih.gov/biosample/SAMN01096076
1
sample type: Cytoplasm,antibody: AGO2,cell line: HeLa,sample fraction: immunoprecipitation
7-9, Quai Saint Bernard
Paris
France
IBPS - Institut Biologie Paris Seine
Eric,,Batsche
Sequences were aligned to the genome (GRCh37) using oligomap (Berninger, P., Gaidatzis, D., van Nimwegen, E. & Zavolan, M. 2008. Computational analysis of small RNA cloning data. Methods 44, 13-21) to find alignments with up to 1 error (replacement, insertion, or deletion). Alignments were filtered to include only the best matches for each sequence. Sequences with >5 alignments were filtered out.,BED tracks were calculated. For each reads their number were indicated followed by an underscore and the length (in nucleotide) of the considered read. Number of clones of the same sequence is indicated in the score label of the BED tracks. sRNAs bound to AGO2 appear in red, sRNAs bound to the control IgG are in blue, and Input are in black.,Genome_build: GRCh37 / hg19,Supplementary_files_format_and_content: BED tracks were calculated. For each reads their number were indicated followed by an underscore and the length (in nucleotide) of the considered read. Number of clones of the same sequence is indicated in the score label of the BED tracks. sRNAs bound to
Following digestion with DNase (RNase free), short RNAs below 100 bp were gel-purified, poly(A)-tailed using poly(A) polymerase, treated with tobacco acid pyrophosphastase, and RNA adapters were ligated to the 5’phosphate of the RNA. cDNA was synthesized and PCR-amplified.
GSM978499
Illumina HiSeq 2000
May 15 2019
cDNA
transcriptomic
RNA-Seq
total RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX171599,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01096077
GSM978499
GSE39748,GSE39749
0.322216
HeLa cells (ATCC)
Public on Aug 22 2012
Jul 30 2012
9606
EC-AGO2
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX171599
https://www.ncbi.nlm.nih.gov/biosample/SAMN01096077
1
sample type: Chromatin,antibody: Input,cell line: HeLa,sample fraction: extract
7-9, Quai Saint Bernard
Paris
France
IBPS - Institut Biologie Paris Seine
Eric,,Batsche
Sequences were aligned to the genome (GRCh37) using oligomap (Berninger, P., Gaidatzis, D., van Nimwegen, E. & Zavolan, M. 2008. Computational analysis of small RNA cloning data. Methods 44, 13-21) to find alignments with up to 1 error (replacement, insertion, or deletion). Alignments were filtered to include only the best matches for each sequence. Sequences with >5 alignments were filtered out.,BED tracks were calculated. For each reads their number were indicated followed by an underscore and the length (in nucleotide) of the considered read. Number of clones of the same sequence is indicated in the score label of the BED tracks. sRNAs bound to AGO2 appear in red, sRNAs bound to the control IgG are in blue, and Input are in black.,Genome_build: GRCh37 / hg19,Supplementary_files_format_and_content: BED tracks were calculated. For each reads their number were indicated followed by an underscore and the length (in nucleotide) of the considered read. Number of clones of the same sequence is indicated in the score label of the BED tracks. sRNAs bound to
Following digestion with DNase (RNase free), short RNAs below 100 bp were gel-purified, poly(A)-tailed using poly(A) polymerase, treated with tobacco acid pyrophosphastase, and RNA adapters were ligated to the 5’phosphate of the RNA. cDNA was synthesized and PCR-amplified.
GSM978500
Illumina HiSeq 2000
May 15 2019
cDNA
transcriptomic
RNA-Seq
total RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX171600,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01096078
GSM978500
GSE39748,GSE39749
0.114519
HeLa cells (ATCC)
Public on Aug 22 2012
Jul 30 2012
9606
Chr-input
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX171600
https://www.ncbi.nlm.nih.gov/biosample/SAMN01096078
1
sample type: Chromatin,antibody: IgG,cell line: HeLa,sample fraction: immunoprecipitation
7-9, Quai Saint Bernard
Paris
France
IBPS - Institut Biologie Paris Seine
Eric,,Batsche
Sequences were aligned to the genome (GRCh37) using oligomap (Berninger, P., Gaidatzis, D., van Nimwegen, E. & Zavolan, M. 2008. Computational analysis of small RNA cloning data. Methods 44, 13-21) to find alignments with up to 1 error (replacement, insertion, or deletion). Alignments were filtered to include only the best matches for each sequence. Sequences with >5 alignments were filtered out.,BED tracks were calculated. For each reads their number were indicated followed by an underscore and the length (in nucleotide) of the considered read. Number of clones of the same sequence is indicated in the score label of the BED tracks. sRNAs bound to AGO2 appear in red, sRNAs bound to the control IgG are in blue, and Input are in black.,Genome_build: GRCh37 / hg19,Supplementary_files_format_and_content: BED tracks were calculated. For each reads their number were indicated followed by an underscore and the length (in nucleotide) of the considered read. Number of clones of the same sequence is indicated in the score label of the BED tracks. sRNAs bound to
Following digestion with DNase (RNase free), short RNAs below 100 bp were gel-purified, poly(A)-tailed using poly(A) polymerase, treated with tobacco acid pyrophosphastase, and RNA adapters were ligated to the 5’phosphate of the RNA. cDNA was synthesized and PCR-amplified.
GSM978501
Illumina HiSeq 2000
May 15 2019
cDNA
transcriptomic
RNA-Seq
total RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX171601,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01096079
GSM978501
GSE39748,GSE39749
0.235022
HeLa cells (ATCC)
Public on Aug 22 2012
Jul 30 2012
9606
Chr-IgG
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX171601
https://www.ncbi.nlm.nih.gov/biosample/SAMN01096079
1
sample type: Chromatin,antibody: AGO2,cell line: HeLa,sample fraction: immunoprecipitation
7-9, Quai Saint Bernard
Paris
France
IBPS - Institut Biologie Paris Seine
Eric,,Batsche
Sequences were aligned to the genome (GRCh37) using oligomap (Berninger, P., Gaidatzis, D., van Nimwegen, E. & Zavolan, M. 2008. Computational analysis of small RNA cloning data. Methods 44, 13-21) to find alignments with up to 1 error (replacement, insertion, or deletion). Alignments were filtered to include only the best matches for each sequence. Sequences with >5 alignments were filtered out.,BED tracks were calculated. For each reads their number were indicated followed by an underscore and the length (in nucleotide) of the considered read. Number of clones of the same sequence is indicated in the score label of the BED tracks. sRNAs bound to AGO2 appear in red, sRNAs bound to the control IgG are in blue, and Input are in black.,Genome_build: GRCh37 / hg19,Supplementary_files_format_and_content: BED tracks were calculated. For each reads their number were indicated followed by an underscore and the length (in nucleotide) of the considered read. Number of clones of the same sequence is indicated in the score label of the BED tracks. sRNAs bound to
Following digestion with DNase (RNase free), short RNAs below 100 bp were gel-purified, poly(A)-tailed using poly(A) polymerase, treated with tobacco acid pyrophosphastase, and RNA adapters were ligated to the 5’phosphate of the RNA. cDNA was synthesized and PCR-amplified.
GSM978502
Illumina HiSeq 2000
May 15 2019
cDNA
transcriptomic
RNA-Seq
total RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX171602,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01096080
GSM978502
GSE39748,GSE39749
0.067478
HeLa cells (ATCC)
Public on Aug 22 2012
Jul 30 2012
9606
Chr-AGO2
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX171602
https://www.ncbi.nlm.nih.gov/biosample/SAMN01096080
1
tissue: placenta from full-term pregnancy,Sex: male
Medical Microbiology and Immunology
Davis
USA
UC Davis
Janine,,LaSalle
Sequencing index was in first 4 bases of sequencing read. For raw fastq files, first four bases were removed and separate fastq files were made for each indexed replicate.,Reads were mapped to the hg18 version of the genome using TopHat (version 1). Parameters: --library-type fr-unstranded –GTF –butterfly-search –no-novel-juncs --prefilter-multihits,Cufflinks was used to assemble the mapped reads into transcripts, omitting reads that did not align to known transcripts. Parameters: --library-type fr-unstranded – GTF –frag-bias-correct –multi-read-correct –frag-len-mean 390 –compatible-hits-norm,Genome_build: hg18,Supplementary_files_format_and_content: fpkm_tracking file from Cufflinks
RNA was extracted using the NuGEN Ovation RNA-Seq System. Indexed adapters were added using the NuGEN Encore NGS Library System I.
GSM978969
Illumina HiSeq 2000
May 15 2019
cDNA
transcriptomic
RNA-Seq
total RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX172467,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01096254
GSM978969
GSE39776,GSE39777
0.152678
placenta
Public on Mar 28 2013
Jul 31 2012
9606
placenta RNA rep1
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX172467
https://www.ncbi.nlm.nih.gov/biosample/SAMN01096254
1
tissue: placenta from full-term pregnancy,Sex: male
Medical Microbiology and Immunology
Davis
USA
UC Davis
Janine,,LaSalle
Sequencing index was in first 4 bases of sequencing read. For raw fastq files, first four bases were removed and separate fastq files were made for each indexed replicate.,Reads were mapped to the hg18 version of the genome using TopHat (version 1). Parameters: --library-type fr-unstranded –GTF –butterfly-search –no-novel-juncs --prefilter-multihits,Cufflinks was used to assemble the mapped reads into transcripts, omitting reads that did not align to known transcripts. Parameters: --library-type fr-unstranded – GTF –frag-bias-correct –multi-read-correct –frag-len-mean 390 –compatible-hits-norm,Genome_build: hg18,Supplementary_files_format_and_content: fpkm_tracking file from Cufflinks
RNA was extracted using the NuGEN Ovation RNA-Seq System. Indexed adapters were added using the NuGEN Encore NGS Library System I.
GSM978970
Illumina HiSeq 2000
May 15 2019
cDNA
transcriptomic
RNA-Seq
total RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX172468,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01096255
GSM978970
GSE39776,GSE39777
0.331448
placenta
Public on Mar 28 2013
Jul 31 2012
9606
placenta RNA rep2
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX172468
https://www.ncbi.nlm.nih.gov/biosample/SAMN01096255
1
datatype: Cage,datatype description: CAGE 5' RNA Tags,rnaextract: longPolyA,rnaextract description: Poly(A)+ RNA longer than 200 nt,biorep: 087C,087C,088C,088C,labexpid: CThi10049,CThi10059,CThi10049,CThi10059,readtype: 1x50,readtype description: Single 50 nt reads,replicate: 3,4,cell sex: M,localization: cytosol,localization description: The fluid between the cells outer membrane and the nucleus,rnaextract: longPolyA,rnaextract description: Poly(A)+ RNA longer than 200 nt,biorep: 087C,labexpid: CThi10049,readtype: 1x50,readtype description: Single 50 nt reads,replicate: 3
300 Pasteur Dr
Stanford
USA
ENCODE DCC
ENCODE,,DCC
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeRikenCage
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeRikenCage
GSM979632
Illumina HiSeq 2000
May 15 2019
CAGE
transcriptomic
RNA-Seq
polyA RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX172609,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01096369,Named Annotation: NA000016902.1 (GSM979632_hg19_wgEncodeRikenCageA549CytosolPapMinusRawRep3.bigWig),Named Annotation: NA000016903.1 (GSM979632_hg19_wgEncodeRikenCageA549CytosolPapMinusRawRep4.bigWig),Named Annotation: NA000016904.1 (GSM979632_hg19_wgEncodeRikenCageA549CytosolPapPlusRawRep3.bigWig),Named Annotation: NA000016905.1 (GSM979632_hg19_wgEncodeRikenCageA549CytosolPapPlusRawRep4.bigWig)
GSM979632
GSE34448
0.019991
A549
Public on Aug 01 2012
Aug 01 2012
9606
RIKEN_Cage_A549_cytosol_longPolyA
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX172609
https://www.ncbi.nlm.nih.gov/biosample/SAMN01096369
1
datatype: Cage,datatype description: CAGE 5' RNA Tags,rnaextract: longPolyA,rnaextract description: Poly(A)+ RNA longer than 200 nt,biorep: 088N,087N,088N,087N,labexpid: CThi10060,CThi10106,CThi10106,CThi10060,readtype: 1x50,readtype description: Single 50 nt reads,replicate: 3,4,cell sex: M,localization: nucleus,localization description: Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA,rnaextract: longPolyA,rnaextract description: Poly(A)+ RNA longer than 200 nt,biorep: 087N,labexpid: CThi10106,readtype: 1x50,readtype description: Single 50 nt reads,replicate: 3
300 Pasteur Dr
Stanford
USA
ENCODE DCC
ENCODE,,DCC
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeRikenCage
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeRikenCage
GSM979633
Illumina HiSeq 2000
May 15 2019
CAGE
transcriptomic
RNA-Seq
polyA RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX172610,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01096370,Named Annotation: NA000016906.1 (GSM979633_hg19_wgEncodeRikenCageA549NucleusPapMinusRawRep3.bigWig),Named Annotation: NA000016907.1 (GSM979633_hg19_wgEncodeRikenCageA549NucleusPapMinusRawRep4.bigWig),Named Annotation: NA000016908.1 (GSM979633_hg19_wgEncodeRikenCageA549NucleusPapPlusRawRep3.bigWig),Named Annotation: NA000016909.1 (GSM979633_hg19_wgEncodeRikenCageA549NucleusPapPlusRawRep4.bigWig)
GSM979633
GSE34448
0.163004
A549
Public on Aug 01 2012
Aug 01 2012
9606
RIKEN_Cage_A549_nucleus_longPolyA
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX172610
https://www.ncbi.nlm.nih.gov/biosample/SAMN01096370
1
datatype: Cage,datatype description: CAGE 5' RNA Tags,rnaextract: longPolyA,rnaextract description: Poly(A)+ RNA longer than 200 nt,biorep: 042WC,041WC,042WC,041WC,labexpid: CThi10023,CThi10024,CThi10024,CThi10023,readtype: 1x50,readtype description: Single 50 nt reads,replicate: 1,2,cell sex: F,localization: cell,localization description: Whole cell,rnaextract: longPolyA,rnaextract description: Poly(A)+ RNA longer than 200 nt,biorep: 041WC,labexpid: CThi10023,readtype: 1x50,readtype description: Single 50 nt reads,replicate: 1
300 Pasteur Dr
Stanford
USA
ENCODE DCC
ENCODE,,DCC
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeRikenCage
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeRikenCage
GSM979634
Illumina HiSeq 2000
May 15 2019
CAGE
transcriptomic
RNA-Seq
polyA RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX172611,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01096371,Named Annotation: NA000016910.1 (GSM979634_hg19_wgEncodeRikenCageCd20CellPapMinusRawRep1.bigWig),Named Annotation: NA000016911.1 (GSM979634_hg19_wgEncodeRikenCageCd20CellPapMinusRawRep2.bigWig),Named Annotation: NA000016912.1 (GSM979634_hg19_wgEncodeRikenCageCd20CellPapPlusRawRep1.bigWig),Named Annotation: NA000016913.1 (GSM979634_hg19_wgEncodeRikenCageCd20CellPapPlusRawRep2.bigWig)
GSM979634
GSE34448
0.012937
CD20+
Public on Aug 01 2012
Aug 01 2012
9606
RIKEN_Cage_CD20+_cell_longPolyA
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX172611
https://www.ncbi.nlm.nih.gov/biosample/SAMN01096371
1
datatype: Cage,datatype description: CAGE 5' RNA Tags,rnaextract: longPolyA,rnaextract description: Poly(A)+ RNA longer than 200 nt,biorep: 058WC,057WC,057WC,058WC,labexpid: CThi10103GAT,CThi10105CTT,CThi10105CTT,CThi10103GAT,readtype: 1x50,readtype description: Single 50 nt reads,replicate: 1,2,cell sex: B,localization: cell,localization description: Whole cell,rnaextract: longPolyA,rnaextract description: Poly(A)+ RNA longer than 200 nt,biorep: 057WC,labexpid: CThi10103GAT,readtype: 1x50,readtype description: Single 50 nt reads,replicate: 1
300 Pasteur Dr
Stanford
USA
ENCODE DCC
ENCODE,,DCC
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeRikenCage
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeRikenCage
GSM979636
Illumina HiSeq 2000
May 15 2019
CAGE
transcriptomic
RNA-Seq
polyA RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX172613,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01096373,Named Annotation: NA000016916.1 (GSM979636_hg19_wgEncodeRikenCageHaoecCellPapMinusRawRep1.bigWig),Named Annotation: NA000016917.1 (GSM979636_hg19_wgEncodeRikenCageHaoecCellPapMinusRawRep2.bigWig),Named Annotation: NA000016918.1 (GSM979636_hg19_wgEncodeRikenCageHaoecCellPapPlusRawRep1.bigWig),Named Annotation: NA000016919.1 (GSM979636_hg19_wgEncodeRikenCageHaoecCellPapPlusRawRep2.bigWig)
GSM979636
GSE34448
0.215808
HAoEC
Public on Aug 01 2012
Aug 01 2012
9606
RIKEN_Cage_HAoEC_cell_longPolyA
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX172613
https://www.ncbi.nlm.nih.gov/biosample/SAMN01096373
1
datatype: Cage,datatype description: CAGE 5' RNA Tags,rnaextract: longPolyA,rnaextract description: Poly(A)+ RNA longer than 200 nt,biorep: 055WC,056WC,056WC,055WC,labexpid: CThi10103CTT,CThi10100CTT,CThi10100CTT,CThi10103CTT,readtype: 1x50,readtype description: Single 50 nt reads,replicate: 1,2,cell sex: B,localization: cell,localization description: Whole cell,rnaextract: longPolyA,rnaextract description: Poly(A)+ RNA longer than 200 nt,biorep: 055WC,labexpid: CThi10100CTT,readtype: 1x50,readtype description: Single 50 nt reads,replicate: 1
300 Pasteur Dr
Stanford
USA
ENCODE DCC
ENCODE,,DCC
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeRikenCage
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeRikenCage
GSM979637
Illumina HiSeq 2000
May 15 2019
CAGE
transcriptomic
RNA-Seq
polyA RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX172614,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01096374,Named Annotation: NA000016920.1 (GSM979637_hg19_wgEncodeRikenCageHaoafCellPapMinusRawRep1.bigWig),Named Annotation: NA000016921.1 (GSM979637_hg19_wgEncodeRikenCageHaoafCellPapMinusRawRep2.bigWig),Named Annotation: NA000016922.1 (GSM979637_hg19_wgEncodeRikenCageHaoafCellPapPlusRawRep1.bigWig),Named Annotation: NA000016923.1 (GSM979637_hg19_wgEncodeRikenCageHaoafCellPapPlusRawRep2.bigWig)
GSM979637
GSE34448
0.137884
HAoAF
Public on Aug 01 2012
Aug 01 2012
9606
RIKEN_Cage_HAoAF_cell_longPolyA
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX172614
https://www.ncbi.nlm.nih.gov/biosample/SAMN01096374
1
datatype: Cage,datatype description: CAGE 5' RNA Tags,rnaextract: longPolyA,rnaextract description: Poly(A)+ RNA longer than 200 nt,biorep: 061WC,062WC,062WC,061WC,labexpid: CThi10103ACA,CThi10100GAT,CThi10103ACA,CThi10100GAT,readtype: 1x50,readtype description: Single 50 nt reads,replicate: 1,2,cell sex: F,localization: cell,localization description: Whole cell,rnaextract: longPolyA,rnaextract description: Poly(A)+ RNA longer than 200 nt,biorep: 061WC,labexpid: CThi10103ACA,readtype: 1x50,readtype description: Single 50 nt reads,replicate: 1
300 Pasteur Dr
Stanford
USA
ENCODE DCC
ENCODE,,DCC
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeRikenCage
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeRikenCage
GSM979638
Illumina HiSeq 2000
May 15 2019
CAGE
transcriptomic
RNA-Seq
polyA RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX172615,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01096375,Named Annotation: NA000016924.1 (GSM979638_hg19_wgEncodeRikenCageHfdpcCellPapMinusRawRep1.bigWig),Named Annotation: NA000016925.1 (GSM979638_hg19_wgEncodeRikenCageHfdpcCellPapMinusRawRep2.bigWig),Named Annotation: NA000016926.1 (GSM979638_hg19_wgEncodeRikenCageHfdpcCellPapPlusRawRep1.bigWig),Named Annotation: NA000016927.1 (GSM979638_hg19_wgEncodeRikenCageHfdpcCellPapPlusRawRep2.bigWig)
GSM979638
GSE34448
0.449405
HFDPC
Public on Aug 01 2012
Aug 01 2012
9606
RIKEN_Cage_HFDPC_cell_longPolyA
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX172615
https://www.ncbi.nlm.nih.gov/biosample/SAMN01096375
1
datatype: Cage,datatype description: CAGE 5' RNA Tags,rnaextract: longPolyA,rnaextract description: Poly(A)+ RNA longer than 200 nt,biorep: 059WC,059WC,060WC,060WC,labexpid: CThi10104CTT,CThi10104ACA,CThi10104ACA,CThi10104CTT,readtype: 1x50,readtype description: Single 50 nt reads,replicate: 1,2,cell sex: M,localization: cell,localization description: Whole cell,rnaextract: longPolyA,rnaextract description: Poly(A)+ RNA longer than 200 nt,biorep: 059WC,labexpid: CThi10104CTT,readtype: 1x50,readtype description: Single 50 nt reads,replicate: 1
300 Pasteur Dr
Stanford
USA
ENCODE DCC
ENCODE,,DCC
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeRikenCage
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeRikenCage
GSM979639
Illumina HiSeq 2000
May 15 2019
CAGE
transcriptomic
RNA-Seq
polyA RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX172616,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01096376,Named Annotation: NA000016928.1 (GSM979639_hg19_wgEncodeRikenCageHchCellPapMinusRawRep1.bigWig),Named Annotation: NA000016929.1 (GSM979639_hg19_wgEncodeRikenCageHchCellPapMinusRawRep2.bigWig),Named Annotation: NA000016930.1 (GSM979639_hg19_wgEncodeRikenCageHchCellPapPlusRawRep1.bigWig),Named Annotation: NA000016931.1 (GSM979639_hg19_wgEncodeRikenCageHchCellPapPlusRawRep2.bigWig)
GSM979639
GSE34448
0.462799
HCH
Public on Aug 01 2012
Aug 01 2012
9606
RIKEN_Cage_HCH_cell_longPolyA
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX172616
https://www.ncbi.nlm.nih.gov/biosample/SAMN01096376
1
datatype: Cage,datatype description: CAGE 5' RNA Tags,rnaextract: longPolyA,rnaextract description: Poly(A)+ RNA longer than 200 nt,biorep: 053WC,054WC,054WC,053WC,labexpid: CThi10037,CThi10036,CThi10036,CThi10037,readtype: 1x50,readtype description: Single 50 nt reads,replicate: 1,2,cell sex: M,localization: cell,localization description: Whole cell,rnaextract: longPolyA,rnaextract description: Poly(A)+ RNA longer than 200 nt,biorep: 053WC,labexpid: CThi10036,readtype: 1x50,readtype description: Single 50 nt reads,replicate: 1
300 Pasteur Dr
Stanford
USA
ENCODE DCC
ENCODE,,DCC
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeRikenCage
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeRikenCage
GSM979640
Illumina HiSeq 2000
May 15 2019
CAGE
transcriptomic
RNA-Seq
polyA RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX172617,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01096377,Named Annotation: NA000016932.1 (GSM979640_hg19_wgEncodeRikenCageHobCellPapMinusRawRep1.bigWig),Named Annotation: NA000016933.1 (GSM979640_hg19_wgEncodeRikenCageHobCellPapMinusRawRep2.bigWig),Named Annotation: NA000016934.1 (GSM979640_hg19_wgEncodeRikenCageHobCellPapPlusRawRep1.bigWig),Named Annotation: NA000016935.1 (GSM979640_hg19_wgEncodeRikenCageHobCellPapPlusRawRep2.bigWig)
GSM979640
GSE34448
0.080713
HOB
Public on Aug 01 2012
Aug 01 2012
9606
RIKEN_Cage_HOB_cell_longPolyA
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX172617
https://www.ncbi.nlm.nih.gov/biosample/SAMN01096377
1
datatype: Cage,datatype description: CAGE 5' RNA Tags,rnaextract: longPolyA,rnaextract description: Poly(A)+ RNA longer than 200 nt,biorep: 063WC,labexpid: CThi10105GAT,readtype: 1x50,readtype description: Single 50 nt reads,cell lineage: ectoderm,cell sex: F,localization: cell,localization description: Whole cell,rnaextract: longPolyA,rnaextract description: Poly(A)+ RNA longer than 200 nt,biorep: 063WC,labexpid: CThi10105GAT,readtype: 1x50,readtype description: Single 50 nt reads,replicate: 1
300 Pasteur Dr
Stanford
USA
ENCODE DCC
ENCODE,,DCC
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeRikenCage
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeRikenCage
GSM979641
Illumina HiSeq 2000
May 15 2019
CAGE
transcriptomic
RNA-Seq
polyA RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX172618,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01096378,Named Annotation: NA000016936.1 (GSM979641_hg19_wgEncodeRikenCageHmepcCellPapMinusRawRep1.bigWig),Named Annotation: NA000016937.1 (GSM979641_hg19_wgEncodeRikenCageHmepcCellPapPlusRawRep1.bigWig)
GSM979641
GSE34448
0.196068
HMEpC
Public on Aug 01 2012
Aug 01 2012
9606
RIKEN_Cage_HMEpC_cell_longPolyA
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX172618
https://www.ncbi.nlm.nih.gov/biosample/SAMN01096378
1
datatype: Cage,datatype description: CAGE 5' RNA Tags,rnaextract: longPolyA,rnaextract description: Poly(A)+ RNA longer than 200 nt,biorep: 073WC,074WC,073WC,074WC,labexpid: CThi10104ATC,CThi10101GAT,CThi10104ATC,CThi10101GAT,readtype: 1x50,readtype description: Single 50 nt reads,replicate: 1,2,cell sex: B,localization: cell,localization description: Whole cell,rnaextract: longPolyA,rnaextract description: Poly(A)+ RNA longer than 200 nt,biorep: 073WC,labexpid: CThi10104ATC,readtype: 1x50,readtype description: Single 50 nt reads,replicate: 1
300 Pasteur Dr
Stanford
USA
ENCODE DCC
ENCODE,,DCC
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeRikenCage
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeRikenCage
GSM979642
Illumina HiSeq 2000
May 15 2019
CAGE
transcriptomic
RNA-Seq
polyA RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX172619,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01096379,Named Annotation: NA000016938.1 (GSM979642_hg19_wgEncodeRikenCageHpiepcCellPapMinusRawRep1.bigWig),Named Annotation: NA000016939.1 (GSM979642_hg19_wgEncodeRikenCageHpiepcCellPapMinusRawRep2.bigWig),Named Annotation: NA000016940.1 (GSM979642_hg19_wgEncodeRikenCageHpiepcCellPapPlusRawRep1.bigWig),Named Annotation: NA000016941.1 (GSM979642_hg19_wgEncodeRikenCageHpiepcCellPapPlusRawRep2.bigWig)
GSM979642
GSE34448
0.125668
HPIEpC
Public on Aug 01 2012
Aug 01 2012
9606
RIKEN_Cage_HPIEpC_cell_longPolyA
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX172619
https://www.ncbi.nlm.nih.gov/biosample/SAMN01096379
1
datatype: Cage,datatype description: CAGE 5' RNA Tags,rnaextract: longPolyA,rnaextract description: Poly(A)+ RNA longer than 200 nt,biorep: 072WC,071WC,072WC,071WC,labexpid: CThi10057,CThi10105ATC,CThi10057,CThi10105ATC,readtype: 1x50,readtype description: Single 50 nt reads,replicate: 1,2,cell sex: B,localization: cell,localization description: Whole cell,rnaextract: longPolyA,rnaextract description: Poly(A)+ RNA longer than 200 nt,biorep: 071WC,labexpid: CThi10057,readtype: 1x50,readtype description: Single 50 nt reads,replicate: 1
300 Pasteur Dr
Stanford
USA
ENCODE DCC
ENCODE,,DCC
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeRikenCage
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeRikenCage
GSM979643
Illumina HiSeq 2000
May 15 2019
CAGE
transcriptomic
RNA-Seq
polyA RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX172620,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01096380,Named Annotation: NA000016942.1 (GSM979643_hg19_wgEncodeRikenCageHpcplCellPapMinusRawRep1.bigWig),Named Annotation: NA000016943.1 (GSM979643_hg19_wgEncodeRikenCageHpcplCellPapMinusRawRep2.bigWig),Named Annotation: NA000016944.1 (GSM979643_hg19_wgEncodeRikenCageHpcplCellPapPlusRawRep1.bigWig),Named Annotation: NA000016945.1 (GSM979643_hg19_wgEncodeRikenCageHpcplCellPapPlusRawRep2.bigWig)
GSM979643
GSE34448
0.299444
HPC-PL
Public on Aug 01 2012
Aug 01 2012
9606
RIKEN_Cage_HPC-PL_cell_longPolyA
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX172620
https://www.ncbi.nlm.nih.gov/biosample/SAMN01096380
1
datatype: Cage,datatype description: CAGE 5' RNA Tags,rnaextract: longPolyA,rnaextract description: Poly(A)+ RNA longer than 200 nt,biorep: 094WC,093WC,093WC,094WC,labexpid: CThi10102ATC,CThi10102ACA,CThi10102ATC,CThi10102ACA,readtype: 1x50,readtype description: Single 50 nt reads,replicate: 1,2,cell sex: M,localization: cell,localization description: Whole cell,rnaextract: longPolyA,rnaextract description: Poly(A)+ RNA longer than 200 nt,biorep: 093WC,labexpid: CThi10102ACA,readtype: 1x50,readtype description: Single 50 nt reads,replicate: 1
300 Pasteur Dr
Stanford
USA
ENCODE DCC
ENCODE,,DCC
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeRikenCage
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeRikenCage
GSM979645
Illumina HiSeq 2000
May 15 2019
CAGE
transcriptomic
RNA-Seq
polyA RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX172622,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01096382,Named Annotation: NA000016948.1 (GSM979645_hg19_wgEncodeRikenCageHsavecCellPapMinusRawRep1.bigWig),Named Annotation: NA000016949.1 (GSM979645_hg19_wgEncodeRikenCageHsavecCellPapMinusRawRep2.bigWig),Named Annotation: NA000016950.1 (GSM979645_hg19_wgEncodeRikenCageHsavecCellPapPlusRawRep1.bigWig),Named Annotation: NA000016951.1 (GSM979645_hg19_wgEncodeRikenCageHsavecCellPapPlusRawRep2.bigWig)
GSM979645
GSE34448
0.122305
HSaVEC
Public on Aug 01 2012
Aug 01 2012
9606
RIKEN_Cage_HSaVEC_cell_longPolyA
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX172622
https://www.ncbi.nlm.nih.gov/biosample/SAMN01096382
1
datatype: Cage,datatype description: CAGE 5' RNA Tags,rnaextract: longPolyA,rnaextract description: Poly(A)+ RNA longer than 200 nt,biorep: 086WC,085WC,086WC,085WC,labexpid: CThi10043,CThi10043,CThi10046,CThi10046,readtype: 1x50,readtype description: Single 50 nt reads,replicate: 3,4,cell sex: F,localization: cell,localization description: Whole cell,rnaextract: longPolyA,rnaextract description: Poly(A)+ RNA longer than 200 nt,biorep: 085WC,labexpid: CThi10043,readtype: 1x50,readtype description: Single 50 nt reads,replicate: 3
300 Pasteur Dr
Stanford
USA
ENCODE DCC
ENCODE,,DCC
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeRikenCage
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeRikenCage
GSM979646
Illumina HiSeq 2000
May 15 2019
CAGE
transcriptomic
RNA-Seq
polyA RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX172623,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01096383,Named Annotation: NA000016952.1 (GSM979646_hg19_wgEncodeRikenCageSknshCellPapMinusRawRep3.bigWig),Named Annotation: NA000016953.1 (GSM979646_hg19_wgEncodeRikenCageSknshCellPapMinusRawRep4.bigWig),Named Annotation: NA000016954.1 (GSM979646_hg19_wgEncodeRikenCageSknshCellPapPlusRawRep3.bigWig),Named Annotation: NA000016955.1 (GSM979646_hg19_wgEncodeRikenCageSknshCellPapPlusRawRep4.bigWig)
GSM979646
GSE34448
0.024784
SK-N-SH
Public on Aug 01 2012
Aug 01 2012
9606
RIKEN_Cage_SK-N-SH_cell_longPolyA
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX172623
https://www.ncbi.nlm.nih.gov/biosample/SAMN01096383
1
datatype: Cage,datatype description: CAGE 5' RNA Tags,rnaextract: longPolyA,rnaextract description: Poly(A)+ RNA longer than 200 nt,biorep: 086N,085N,085N,086N,labexpid: CThi10048,CThi10045,CThi10048,CThi10045,readtype: 1x50,readtype description: Single 50 nt reads,replicate: 3,4,cell sex: F,localization: nucleus,localization description: Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA,rnaextract: longPolyA,rnaextract description: Poly(A)+ RNA longer than 200 nt,biorep: 085N,labexpid: CThi10045,readtype: 1x50,readtype description: Single 50 nt reads,replicate: 3
300 Pasteur Dr
Stanford
USA
ENCODE DCC
ENCODE,,DCC
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeRikenCage
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeRikenCage
GSM979647
Illumina HiSeq 2000
May 15 2019
CAGE
transcriptomic
RNA-Seq
polyA RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX172624,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01096384,Named Annotation: NA000016956.1 (GSM979647_hg19_wgEncodeRikenCageSknshNucleusPapMinusRawRep3.bigWig),Named Annotation: NA000016957.1 (GSM979647_hg19_wgEncodeRikenCageSknshNucleusPapMinusRawRep4.bigWig),Named Annotation: NA000016958.1 (GSM979647_hg19_wgEncodeRikenCageSknshNucleusPapPlusRawRep3.bigWig),Named Annotation: NA000016959.1 (GSM979647_hg19_wgEncodeRikenCageSknshNucleusPapPlusRawRep4.bigWig)
GSM979647
GSE34448
0.023794
SK-N-SH
Public on Aug 01 2012
Aug 01 2012
9606
RIKEN_Cage_SK-N-SH_nucleus_longPolyA
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX172624
https://www.ncbi.nlm.nih.gov/biosample/SAMN01096384
1
datatype: Cage,datatype description: CAGE 5' RNA Tags,rnaextract: longPolyA,rnaextract description: Poly(A)+ RNA longer than 200 nt,biorep: 085C,085C,086C,086C,labexpid: CThi10044,CThi10047,CThi10044,CThi10047,readtype: 1x50,readtype description: Single 50 nt reads,replicate: 3,4,cell sex: F,localization: cytosol,localization description: The fluid between the cells outer membrane and the nucleus,rnaextract: longPolyA,rnaextract description: Poly(A)+ RNA longer than 200 nt,biorep: 085C,labexpid: CThi10044,readtype: 1x50,readtype description: Single 50 nt reads,replicate: 3
300 Pasteur Dr
Stanford
USA
ENCODE DCC
ENCODE,,DCC
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeRikenCage
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeRikenCage
GSM979648
Illumina HiSeq 2000
May 15 2019
CAGE
transcriptomic
RNA-Seq
polyA RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX172625,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01096385,Named Annotation: NA000016960.1 (GSM979648_hg19_wgEncodeRikenCageSknshCytosolPapMinusRawRep3.bigWig),Named Annotation: NA000016961.1 (GSM979648_hg19_wgEncodeRikenCageSknshCytosolPapMinusRawRep4.bigWig),Named Annotation: NA000016962.1 (GSM979648_hg19_wgEncodeRikenCageSknshCytosolPapPlusRawRep3.bigWig),Named Annotation: NA000016963.1 (GSM979648_hg19_wgEncodeRikenCageSknshCytosolPapPlusRawRep4.bigWig)
GSM979648
GSE34448
0.072941
SK-N-SH
Public on Aug 01 2012
Aug 01 2012
9606
RIKEN_Cage_SK-N-SH_cytosol_longPolyA
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX172625
https://www.ncbi.nlm.nih.gov/biosample/SAMN01096385
1
datatype: Cage,datatype description: CAGE 5' RNA Tags,rnaextract: longPolyA,rnaextract description: Poly(A)+ RNA longer than 200 nt,biorep: 083WC,084WC,083WC,084WC,labexpid: CThi10056,CThi10102GAT,CThi10056,CThi10102GAT,readtype: 1x50,readtype description: Single 50 nt reads,replicate: 1,2,cell sex: B,localization: cell,localization description: Whole cell,rnaextract: longPolyA,rnaextract description: Poly(A)+ RNA longer than 200 nt,biorep: 083WC,labexpid: CThi10056,readtype: 1x50,readtype description: Single 50 nt reads,replicate: 1
300 Pasteur Dr
Stanford
USA
ENCODE DCC
ENCODE,,DCC
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeRikenCage
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeRikenCage
GSM979649
Illumina HiSeq 2000
May 15 2019
CAGE
transcriptomic
RNA-Seq
polyA RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX172626,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01096386,Named Annotation: NA000016964.1 (GSM979649_hg19_wgEncodeRikenCageNhemm2CellPapMinusRawRep1.bigWig),Named Annotation: NA000016965.1 (GSM979649_hg19_wgEncodeRikenCageNhemm2CellPapMinusRawRep2.bigWig),Named Annotation: NA000016966.1 (GSM979649_hg19_wgEncodeRikenCageNhemm2CellPapPlusRawRep1.bigWig),Named Annotation: NA000016967.1 (GSM979649_hg19_wgEncodeRikenCageNhemm2CellPapPlusRawRep2.bigWig)
GSM979649
GSE34448
0.013965
NHEM_M2
Public on Aug 01 2012
Aug 01 2012
9606
RIKEN_Cage_NHEM_M2_cell_longPolyA
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX172626
https://www.ncbi.nlm.nih.gov/biosample/SAMN01096386
1
datatype: Cage,datatype description: CAGE 5' RNA Tags,rnaextract: longPolyA,rnaextract description: Poly(A)+ RNA longer than 200 nt,biorep: 069WC,069WC,070WC,070WC,labexpid: CThi10101CTT,CThi10101CTT,CThi10100ATC,CThi10100ATC,readtype: 1x50,readtype description: Single 50 nt reads,replicate: 1,2,cell sex: B,localization: cell,localization description: Whole cell,rnaextract: longPolyA,rnaextract description: Poly(A)+ RNA longer than 200 nt,biorep: 069WC,labexpid: CThi10101CTT,readtype: 1x50,readtype description: Single 50 nt reads,replicate: 1
300 Pasteur Dr
Stanford
USA
ENCODE DCC
ENCODE,,DCC
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeRikenCage
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeRikenCage
GSM979650
Illumina HiSeq 2000
May 15 2019
CAGE
transcriptomic
RNA-Seq
polyA RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX172627,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01096387,Named Annotation: NA000016968.1 (GSM979650_hg19_wgEncodeRikenCageHmscucCellPapMinusRawRep1.bigWig),Named Annotation: NA000016969.1 (GSM979650_hg19_wgEncodeRikenCageHmscucCellPapMinusRawRep2.bigWig),Named Annotation: NA000016970.1 (GSM979650_hg19_wgEncodeRikenCageHmscucCellPapPlusRawRep1.bigWig),Named Annotation: NA000016971.1 (GSM979650_hg19_wgEncodeRikenCageHmscucCellPapPlusRawRep2.bigWig)
GSM979650
GSE34448
0.125782
hMSC-UC
Public on Aug 01 2012
Aug 01 2012
9606
RIKEN_Cage_hMSC-UC_cell_longPolyA
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX172627
https://www.ncbi.nlm.nih.gov/biosample/SAMN01096387
1
datatype: Cage,datatype description: CAGE 5' RNA Tags,rnaextract: longPolyA,rnaextract description: Poly(A)+ RNA longer than 200 nt,biorep: 067WC,068WC,068WC,067WC,labexpid: CThi10100ACA,CThi10103ATC,CThi10100ACA,CThi10103ATC,readtype: 1x50,readtype description: Single 50 nt reads,replicate: 1,2,cell sex: B,localization: cell,localization description: Whole cell,rnaextract: longPolyA,rnaextract description: Poly(A)+ RNA longer than 200 nt,biorep: 067WC,labexpid: CThi10103ATC,readtype: 1x50,readtype description: Single 50 nt reads,replicate: 1
300 Pasteur Dr
Stanford
USA
ENCODE DCC
ENCODE,,DCC
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeRikenCage
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeRikenCage
GSM979651
Illumina HiSeq 2000
May 15 2019
CAGE
transcriptomic
RNA-Seq
polyA RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX172628,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01096388,Named Annotation: NA000016972.1 (GSM979651_hg19_wgEncodeRikenCageHmscbmCellPapMinusRawRep1.bigWig),Named Annotation: NA000016973.1 (GSM979651_hg19_wgEncodeRikenCageHmscbmCellPapMinusRawRep2.bigWig),Named Annotation: NA000016974.1 (GSM979651_hg19_wgEncodeRikenCageHmscbmCellPapPlusRawRep1.bigWig),Named Annotation: NA000016975.1 (GSM979651_hg19_wgEncodeRikenCageHmscbmCellPapPlusRawRep2.bigWig)
GSM979651
GSE34448
0.152539
hMSC-BM
Public on Aug 01 2012
Aug 01 2012
9606
RIKEN_Cage_hMSC-BM_cell_longPolyA
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX172628
https://www.ncbi.nlm.nih.gov/biosample/SAMN01096388
1
datatype: Cage,datatype description: CAGE 5' RNA Tags,rnaextract: longPolyA,rnaextract description: Poly(A)+ RNA longer than 200 nt,biorep: 065WC,065WC,066WC,066WC,labexpid: CThi10105ACA,CThi10104GAT,CThi10105ACA,CThi10104GAT,readtype: 1x50,readtype description: Single 50 nt reads,replicate: 1,2,cell sex: F,localization: cell,localization description: Whole cell,rnaextract: longPolyA,rnaextract description: Poly(A)+ RNA longer than 200 nt,biorep: 065WC,labexpid: CThi10105ACA,readtype: 1x50,readtype description: Single 50 nt reads,replicate: 1
300 Pasteur Dr
Stanford
USA
ENCODE DCC
ENCODE,,DCC
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeRikenCage
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeRikenCage
GSM979652
Illumina HiSeq 2000
May 15 2019
CAGE
transcriptomic
RNA-Seq
polyA RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX172629,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01096389,Named Annotation: NA000016976.1 (GSM979652_hg19_wgEncodeRikenCageHmscatCellPapMinusRawRep1.bigWig),Named Annotation: NA000016977.1 (GSM979652_hg19_wgEncodeRikenCageHmscatCellPapMinusRawRep2.bigWig),Named Annotation: NA000016978.1 (GSM979652_hg19_wgEncodeRikenCageHmscatCellPapPlusRawRep1.bigWig),Named Annotation: NA000016979.1 (GSM979652_hg19_wgEncodeRikenCageHmscatCellPapPlusRawRep2.bigWig)
GSM979652
GSE34448
0.300144
hMSC-AT
Public on Aug 01 2012
Aug 01 2012
9606
RIKEN_Cage_hMSC-AT_cell_longPolyA
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX172629
https://www.ncbi.nlm.nih.gov/biosample/SAMN01096389
1
datatype: Cage,datatype description: CAGE 5' RNA Tags,rnaextract: longPolyA,rnaextract description: Poly(A)+ RNA longer than 200 nt,biorep: 047WC,048WC,047WC,048WC,labexpid: CThi10031,CThi10030,CThi10030,CThi10031,readtype: 1x50,readtype description: Single 50 nt reads,replicate: 1,2,cell sex: B,localization: cell,localization description: Whole cell,rnaextract: longPolyA,rnaextract description: Poly(A)+ RNA longer than 200 nt,biorep: 047WC,labexpid: CThi10030,readtype: 1x50,readtype description: Single 50 nt reads,replicate: 1
300 Pasteur Dr
Stanford
USA
ENCODE DCC
ENCODE,,DCC
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeRikenCage
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeRikenCage
GSM979653
Illumina HiSeq 2000
May 15 2019
CAGE
transcriptomic
RNA-Seq
polyA RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX172630,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01096390,Named Annotation: NA000016980.1 (GSM979653_hg19_wgEncodeRikenCageSkmcCellPapMinusRawRep1.bigWig),Named Annotation: NA000016981.1 (GSM979653_hg19_wgEncodeRikenCageSkmcCellPapMinusRawRep2.bigWig),Named Annotation: NA000016982.1 (GSM979653_hg19_wgEncodeRikenCageSkmcCellPapPlusRawRep1.bigWig),Named Annotation: NA000016983.1 (GSM979653_hg19_wgEncodeRikenCageSkmcCellPapPlusRawRep2.bigWig)
GSM979653
GSE34448
0.051746
SkMC
Public on Aug 01 2012
Aug 01 2012
9606
RIKEN_Cage_SkMC_cell_longPolyA
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX172630
https://www.ncbi.nlm.nih.gov/biosample/SAMN01096390
1
datatype: Cage,datatype description: CAGE 5' RNA Tags,rnaextract: longPolyA,rnaextract description: Poly(A)+ RNA longer than 200 nt,biorep: 089N,090N,089N,090N,labexpid: CThi10052,CThi10054,CThi10054,CThi10052,readtype: 1x50,readtype description: Single 50 nt reads,replicate: 3,4,cell sex: F,localization: nucleus,localization description: Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA,rnaextract: longPolyA,rnaextract description: Poly(A)+ RNA longer than 200 nt,biorep: 089N,labexpid: CThi10052,readtype: 1x50,readtype description: Single 50 nt reads,replicate: 3
300 Pasteur Dr
Stanford
USA
ENCODE DCC
ENCODE,,DCC
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeRikenCage
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeRikenCage
GSM979654
Illumina HiSeq 2000
May 15 2019
CAGE
transcriptomic
RNA-Seq
polyA RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX172631,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01096391,Named Annotation: NA000016984.1 (GSM979654_hg19_wgEncodeRikenCageMcf7NucleusPapMinusRawRep3.bigWig),Named Annotation: NA000016985.1 (GSM979654_hg19_wgEncodeRikenCageMcf7NucleusPapMinusRawRep4.bigWig),Named Annotation: NA000016986.1 (GSM979654_hg19_wgEncodeRikenCageMcf7NucleusPapPlusRawRep3.bigWig),Named Annotation: NA000016987.1 (GSM979654_hg19_wgEncodeRikenCageMcf7NucleusPapPlusRawRep4.bigWig)
GSM979654
GSE34448
0.024227
MCF-7
Public on Aug 01 2012
Aug 01 2012
9606
RIKEN_Cage_MCF-7_nucleus_longPolyA
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX172631
https://www.ncbi.nlm.nih.gov/biosample/SAMN01096391
1
datatype: Cage,datatype description: CAGE 5' RNA Tags,rnaextract: longPolyA,rnaextract description: Poly(A)+ RNA longer than 200 nt,biorep: 039WC,039WC,040WC,040WC,labexpid: CThi10021,CThi10022,CThi10022,CThi10021,readtype: 1x50,readtype description: Single 50 nt reads,replicate: 1,2,cell sex: F,localization: cell,localization description: Whole cell,rnaextract: longPolyA,rnaextract description: Poly(A)+ RNA longer than 200 nt,biorep: 039WC,labexpid: CThi10021,readtype: 1x50,readtype description: Single 50 nt reads,replicate: 1
300 Pasteur Dr
Stanford
USA
ENCODE DCC
ENCODE,,DCC
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeRikenCage
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeRikenCage
GSM979655
Illumina HiSeq 2000
May 15 2019
CAGE
transcriptomic
RNA-Seq
polyA RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX172632,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01096392,Named Annotation: NA000016988.1 (GSM979655_hg19_wgEncodeRikenCageMonocd14CellPapMinusRawRep1.bigWig),Named Annotation: NA000016989.1 (GSM979655_hg19_wgEncodeRikenCageMonocd14CellPapMinusRawRep2.bigWig),Named Annotation: NA000016990.1 (GSM979655_hg19_wgEncodeRikenCageMonocd14CellPapPlusRawRep1.bigWig),Named Annotation: NA000016991.1 (GSM979655_hg19_wgEncodeRikenCageMonocd14CellPapPlusRawRep2.bigWig)
GSM979655
GSE34448
0
Monocytes-CD14+
Public on Aug 01 2012
Aug 01 2012
9606
RIKEN_Cage_Monocytes-CD14+_cell_longPolyA
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX172632
https://www.ncbi.nlm.nih.gov/biosample/SAMN01096392
1
datatype: Cage,datatype description: CAGE 5' RNA Tags,rnaextract: longPolyA,rnaextract description: Poly(A)+ RNA longer than 200 nt,biorep: 045WC,045WC,046WC,046WC,labexpid: CThi10016,CThi10018,CThi10018,CThi10016,readtype: 1x50,readtype description: Single 50 nt reads,replicate: 1,2,cell sex: F,localization: cell,localization description: Whole cell,rnaextract: longPolyA,rnaextract description: Poly(A)+ RNA longer than 200 nt,biorep: 045WC,labexpid: CThi10016,readtype: 1x50,readtype description: Single 50 nt reads,replicate: 1
300 Pasteur Dr
Stanford
USA
ENCODE DCC
ENCODE,,DCC
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeRikenCage
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeRikenCage
GSM979656
Illumina HiSeq 2000
May 15 2019
CAGE
transcriptomic
RNA-Seq
polyA RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX172633,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01096393,Named Annotation: NA000016992.1 (GSM979656_hg19_wgEncodeRikenCageImr90CellPapMinusRawRep1.bigWig),Named Annotation: NA000016993.1 (GSM979656_hg19_wgEncodeRikenCageImr90CellPapMinusRawRep2.bigWig),Named Annotation: NA000016994.1 (GSM979656_hg19_wgEncodeRikenCageImr90CellPapPlusRawRep1.bigWig),Named Annotation: NA000016995.1 (GSM979656_hg19_wgEncodeRikenCageImr90CellPapPlusRawRep2.bigWig)
GSM979656
GSE34448
0.104833
IMR90
Public on Aug 01 2012
Aug 01 2012
9606
RIKEN_Cage_IMR90_cell_longPolyA
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX172633
https://www.ncbi.nlm.nih.gov/biosample/SAMN01096393
1
datatype: Cage,datatype description: CAGE 5' RNA Tags,rnaextract: longPolyA,rnaextract description: Poly(A)+ RNA longer than 200 nt,biorep: 089C,090C,089C,090C,labexpid: CThi10053,CThi10051,CThi10053,CThi10051,readtype: 1x50,readtype description: Single 50 nt reads,replicate: 3,4,cell sex: F,localization: cytosol,localization description: The fluid between the cells outer membrane and the nucleus,rnaextract: longPolyA,rnaextract description: Poly(A)+ RNA longer than 200 nt,biorep: 089C,labexpid: CThi10051,readtype: 1x50,readtype description: Single 50 nt reads,replicate: 3
300 Pasteur Dr
Stanford
USA
ENCODE DCC
ENCODE,,DCC
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeRikenCage
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeRikenCage
GSM979657
Illumina HiSeq 2000
May 15 2019
CAGE
transcriptomic
RNA-Seq
polyA RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX172634,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01096394,Named Annotation: NA000016996.1 (GSM979657_hg19_wgEncodeRikenCageMcf7CytosolPapMinusRawRep3.bigWig),Named Annotation: NA000016997.1 (GSM979657_hg19_wgEncodeRikenCageMcf7CytosolPapMinusRawRep4.bigWig),Named Annotation: NA000016998.1 (GSM979657_hg19_wgEncodeRikenCageMcf7CytosolPapPlusRawRep3.bigWig),Named Annotation: NA000016999.1 (GSM979657_hg19_wgEncodeRikenCageMcf7CytosolPapPlusRawRep4.bigWig)
GSM979657
GSE34448
0
MCF-7
Public on Aug 01 2012
Aug 01 2012
9606
RIKEN_Cage_MCF-7_cytosol_longPolyA
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX172634
https://www.ncbi.nlm.nih.gov/biosample/SAMN01096394
1
datatype: Cage,datatype description: CAGE 5' RNA Tags,rnaextract: longPolyA,rnaextract description: Poly(A)+ RNA longer than 200 nt,biorep: 045C,046C,046C,045C,labexpid: CThi10017,CThi10019,CThi10019,CThi10017,readtype: 1x50,readtype description: Single 50 nt reads,replicate: 1,2,cell sex: F,localization: cytosol,localization description: The fluid between the cells outer membrane and the nucleus,rnaextract: longPolyA,rnaextract description: Poly(A)+ RNA longer than 200 nt,biorep: 045C,labexpid: CThi10017,readtype: 1x50,readtype description: Single 50 nt reads,replicate: 1
300 Pasteur Dr
Stanford
USA
ENCODE DCC
ENCODE,,DCC
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeRikenCage
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeRikenCage
GSM979658
Illumina HiSeq 2000
May 15 2019
CAGE
transcriptomic
RNA-Seq
polyA RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX172635,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01096395,Named Annotation: NA000017000.1 (GSM979658_hg19_wgEncodeRikenCageImr90CytosolPapMinusRawRep1.bigWig),Named Annotation: NA000017001.1 (GSM979658_hg19_wgEncodeRikenCageImr90CytosolPapMinusRawRep2.bigWig),Named Annotation: NA000017002.1 (GSM979658_hg19_wgEncodeRikenCageImr90CytosolPapPlusRawRep1.bigWig),Named Annotation: NA000017003.1 (GSM979658_hg19_wgEncodeRikenCageImr90CytosolPapPlusRawRep2.bigWig)
GSM979658
GSE34448
0.137849
IMR90
Public on Aug 01 2012
Aug 01 2012
9606
RIKEN_Cage_IMR90_cytosol_longPolyA
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX172635
https://www.ncbi.nlm.nih.gov/biosample/SAMN01096395
1
datatype: Cage,datatype description: CAGE 5' RNA Tags,rnaextract: longPolyA,rnaextract description: Poly(A)+ RNA longer than 200 nt,biorep: 045N,046N,045N,046N,labexpid: CThi10026,CThi10025,CThi10026,CThi10025,readtype: 1x50,readtype description: Single 50 nt reads,replicate: 1,2,cell sex: F,localization: nucleus,localization description: Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA,rnaextract: longPolyA,rnaextract description: Poly(A)+ RNA longer than 200 nt,biorep: 045N,labexpid: CThi10025,readtype: 1x50,readtype description: Single 50 nt reads,replicate: 1
300 Pasteur Dr
Stanford
USA
ENCODE DCC
ENCODE,,DCC
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeRikenCage
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeRikenCage
GSM979659
Illumina HiSeq 2000
May 15 2019
CAGE
transcriptomic
RNA-Seq
polyA RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX172636,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01096396,Named Annotation: NA000017004.1 (GSM979659_hg19_wgEncodeRikenCageImr90NucleusPapMinusRawRep1.bigWig),Named Annotation: NA000017005.1 (GSM979659_hg19_wgEncodeRikenCageImr90NucleusPapMinusRawRep2.bigWig),Named Annotation: NA000017006.1 (GSM979659_hg19_wgEncodeRikenCageImr90NucleusPapPlusRawRep1.bigWig),Named Annotation: NA000017007.1 (GSM979659_hg19_wgEncodeRikenCageImr90NucleusPapPlusRawRep2.bigWig)
GSM979659
GSE34448
0.121164
IMR90
Public on Aug 01 2012
Aug 01 2012
9606
RIKEN_Cage_IMR90_nucleus_longPolyA
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX172636
https://www.ncbi.nlm.nih.gov/biosample/SAMN01096396
1
datatype: Cage,datatype description: CAGE 5' RNA Tags,rnaextract: longPolyA,rnaextract description: Poly(A)+ RNA longer than 200 nt,biorep: 051WC,052WC,051WC,052WC,labexpid: CThi10035,CThi10034,CThi10034,CThi10035,readtype: 1x50,readtype description: Single 50 nt reads,replicate: 1,2,localization: cell,localization description: Whole cell,rnaextract: longPolyA,rnaextract description: Poly(A)+ RNA longer than 200 nt,biorep: 051WC,labexpid: CThi10034,readtype: 1x50,readtype description: Single 50 nt reads,replicate: 1
300 Pasteur Dr
Stanford
USA
ENCODE DCC
ENCODE,,DCC
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeRikenCage
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeRikenCage
GSM979660
Illumina HiSeq 2000
May 15 2019
CAGE
transcriptomic
RNA-Seq
polyA RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX172637,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01096397,Named Annotation: NA000017008.1 (GSM979660_hg19_wgEncodeRikenCageHvmfCellPapMinusRawRep1.bigWig),Named Annotation: NA000017009.1 (GSM979660_hg19_wgEncodeRikenCageHvmfCellPapMinusRawRep2.bigWig),Named Annotation: NA000017010.1 (GSM979660_hg19_wgEncodeRikenCageHvmfCellPapPlusRawRep1.bigWig),Named Annotation: NA000017011.1 (GSM979660_hg19_wgEncodeRikenCageHvmfCellPapPlusRawRep2.bigWig)
GSM979660
GSE34448
0.109409
HVMF
Public on Aug 01 2012
Aug 01 2012
9606
RIKEN_Cage_HVMF_cell_longPolyA
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX172637
https://www.ncbi.nlm.nih.gov/biosample/SAMN01096397
1
datatype: Cage,datatype description: CAGE 5' RNA Tags,rnaextract: longPolyA,rnaextract description: Poly(A)+ RNA longer than 200 nt,biorep: 080WC,079WC,080WC,079WC,labexpid: CThi10101ACA,CThi10101ATC,CThi10101ATC,CThi10101ACA,readtype: 1x50,readtype description: Single 50 nt reads,replicate: 1,2,cell sex: B,localization: cell,localization description: Whole cell,rnaextract: longPolyA,rnaextract description: Poly(A)+ RNA longer than 200 nt,biorep: 079WC,labexpid: CThi10101ACA,readtype: 1x50,readtype description: Single 50 nt reads,replicate: 1
300 Pasteur Dr
Stanford
USA
ENCODE DCC
ENCODE,,DCC
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeRikenCage
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeRikenCage
GSM979661
Illumina HiSeq 2000
May 15 2019
CAGE
transcriptomic
RNA-Seq
polyA RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX172638,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01096398,Named Annotation: NA000017012.1 (GSM979661_hg19_wgEncodeRikenCageHwpCellPapMinusRawRep1.bigWig),Named Annotation: NA000017013.1 (GSM979661_hg19_wgEncodeRikenCageHwpCellPapMinusRawRep2.bigWig),Named Annotation: NA000017014.1 (GSM979661_hg19_wgEncodeRikenCageHwpCellPapPlusRawRep1.bigWig),Named Annotation: NA000017015.1 (GSM979661_hg19_wgEncodeRikenCageHwpCellPapPlusRawRep2.bigWig)
GSM979661
GSE34448
0.045019
HWP
Public on Aug 01 2012
Aug 01 2012
9606
RIKEN_Cage_HWP_cell_longPolyA
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX172638
https://www.ncbi.nlm.nih.gov/biosample/SAMN01096398