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ENCSR385TMY

ENCSR ENCODE
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RNA-seq on HepG2 cells treated with an shRNA knockdown against RBM17. (RBM17_BGHLV26)

Organism: Homo sapiens
Experiment Types:
shRNA RNA-seq
Status: released
Contact: Brenton Graveley, UConn

Summary

shRNA RNA-seq of RBM17 in Homo sapiens HepG2 expressing RNAi targeting H. sapiens RBM17

Overall Design

RNA-seq on HepG2 cells treated with an shRNA knockdown against RBM17. (RBM17_BGHLV26)

Analysis

View Data Processing
Analysis page is available for ENCSR385TMY.

Dataset Citations (3)

PubMed citation (PMID 32728046)
PubMed citation (PMID 32727537)
A large-scale binding and functional map of human RNA-binding proteins.
PMID 32728246 · 2020 · Nature
Eric L Van Nostrand, Peter Freese, Gabriel A Pratt, Xiaofeng Wang, Xintao Wei, Rui Xiao, Steven M Blue, Jia-Yu Chen, Neal A L Cody, Daniel Dominguez, Sara Olson, Balaji Sundararaman, Lijun Zhan, Cassandra Bazile, Louis Philip Benoit Bouvrette, Julie Bergalet, Michael O Duff, Keri E Garcia, Chelsea Gelboin-Burkhart, Myles Hochman, Nicole J Lambert, Hairi Li, Michael P McGurk, Thai B Nguyen, Tsultrim Palden, Ines Rabano, Shashank Sathe, Rebecca Stanton, Amanda Su, Ruth Wang, Brian A Yee, Bing Zhou, Ashley L Louie, Stefan Aigner, Xiang-Dong Fu, Eric Lécuyer, Christopher B Burge, Brenton R Graveley, Gene W Yeo

ENCODE Metadata

Total file size: 126.8 GB
Assay: shRNA RNA-seq
Target: RBM17
Biosample: Homo sapiens HepG2 expressing RNAi targeting H. sapiens RBM17
Files: 92
Unique ENC file IDs: 92
File Formats
bigWig (48) tsv (19) bam (18) fastq (4) tar (3)
Output types (11)
alignments (12) minus strand signal of all reads (12) minus strand signal of unique reads (12) plus strand signal of all reads (12) plus strand signal of unique reads (12) transcript quantifications (8) gene quantifications (6) transcriptome alignments (6) differential expression quantifications (5) reads (4) differential splicing quantifications (3)

Linked Publications (1)

A large-scale binding and functional map of human RNA-binding proteins.
Nature · 2020

Data Files (92)

Accession File Name Stored Type Output Type Mapping Assembly Size Download
ENCFF009JNM ENCFF009JNM.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 5.1 GB link
ENCFF194RBA ENCFF194RBA.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 5.5 GB link
ENCFF596OUL ENCFF596OUL.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 6.2 GB link
ENCFF916JAJ ENCFF916JAJ.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 4.5 GB link
ENCFF218XYS ENCFF218XYS.bam bam (alignments); assembly: GRCh38; genome annotation: V29 alignments GRCh38 6.2 GB link
ENCFF721OHZ ENCFF721OHZ.bam bam (alignments); assembly: GRCh38; genome annotation: V29 alignments GRCh38 5.5 GB link
ENCFF397HZZ ENCFF397HZZ.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 4.5 GB link
ENCFF442JOE ENCFF442JOE.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 6.0 GB link
ENCFF522UFE ENCFF522UFE.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 4.5 GB link
ENCFF665YCW ENCFF665YCW.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 5.0 GB link
ENCFF922UJZ ENCFF922UJZ.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 5.0 GB link
ENCFF993AIW ENCFF993AIW.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 5.4 GB link
ENCFF324OFN ENCFF324OFN.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V24 transcriptome alignments GRCh38 7.8 GB link
ENCFF786BKM ENCFF786BKM.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V24 transcriptome alignments GRCh38 6.9 GB link
ENCFF277UYY ENCFF277UYY.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V29 transcriptome alignments GRCh38 8.8 GB link
ENCFF621MNB ENCFF621MNB.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V29 transcriptome alignments GRCh38 7.9 GB link
ENCFF490JWU ENCFF490JWU.bam bam (transcriptome alignments); assembly: hg19; genome annotation: V19 transcriptome alignments hg19 6.9 GB link
ENCFF939TRZ ENCFF939TRZ.bam bam (transcriptome alignments); assembly: hg19; genome annotation: V19 transcriptome alignments hg19 7.7 GB link
ENCFF109PXI ENCFF109PXI.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 70.1 MB link
ENCFF113MMI ENCFF113MMI.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 90.9 MB link
ENCFF369JLQ ENCFF369JLQ.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 80.5 MB link
ENCFF713SBM ENCFF713SBM.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 79.0 MB link
ENCFF103CCY ENCFF103CCY.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V29 minus strand signal of all reads GRCh38 79.1 MB link
ENCFF414JYP ENCFF414JYP.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V29 minus strand signal of all reads GRCh38 90.9 MB link
ENCFF099PJS ENCFF099PJS.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 72.1 MB link
ENCFF363OMD ENCFF363OMD.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 82.4 MB link
ENCFF479FWV ENCFF479FWV.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 78.3 MB link
ENCFF546RBP ENCFF546RBP.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 91.1 MB link
ENCFF778AFW ENCFF778AFW.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 80.3 MB link
ENCFF810XDT ENCFF810XDT.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 69.2 MB link
ENCFF019ENB ENCFF019ENB.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 81.0 MB link
ENCFF634WDN ENCFF634WDN.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 66.1 MB link
ENCFF655VTG ENCFF655VTG.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 71.1 MB link
ENCFF829YOU ENCFF829YOU.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 75.9 MB link
ENCFF365OWP ENCFF365OWP.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 minus strand signal of unique reads GRCh38 71.1 MB link
ENCFF846PGW ENCFF846PGW.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 minus strand signal of unique reads GRCh38 80.9 MB link
ENCFF020XQG ENCFF020XQG.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 70.4 MB link
ENCFF041JAJ ENCFF041JAJ.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 63.7 MB link
ENCFF137TDF ENCFF137TDF.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 77.0 MB link
ENCFF547JCQ ENCFF547JCQ.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 74.2 MB link
ENCFF711CQE ENCFF711CQE.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 66.2 MB link
ENCFF720FYD ENCFF720FYD.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 80.6 MB link
ENCFF455JEN ENCFF455JEN.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 80.5 MB link
ENCFF555SCV ENCFF555SCV.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 82.2 MB link
ENCFF595UEQ ENCFF595UEQ.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 71.6 MB link
ENCFF732YIZ ENCFF732YIZ.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 92.7 MB link
ENCFF047DGC ENCFF047DGC.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V29 plus strand signal of all reads GRCh38 80.6 MB link
ENCFF088MTP ENCFF088MTP.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V29 plus strand signal of all reads GRCh38 92.7 MB link
ENCFF100GSI ENCFF100GSI.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 70.6 MB link
ENCFF122YTH ENCFF122YTH.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 92.7 MB link
ENCFF182PAM ENCFF182PAM.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 84.2 MB link
ENCFF425QSF ENCFF425QSF.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 82.2 MB link
ENCFF832VDR ENCFF832VDR.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 73.6 MB link
ENCFF998AJM ENCFF998AJM.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 79.7 MB link
ENCFF311VPH ENCFF311VPH.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 68.0 MB link
ENCFF384ADP ENCFF384ADP.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 78.0 MB link
ENCFF479ZDR ENCFF479ZDR.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 83.3 MB link
ENCFF488BJN ENCFF488BJN.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 73.1 MB link
ENCFF829NJK ENCFF829NJK.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 plus strand signal of unique reads GRCh38 83.2 MB link
ENCFF920BIQ ENCFF920BIQ.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 plus strand signal of unique reads GRCh38 73.1 MB link
ENCFF042KTF ENCFF042KTF.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 68.1 MB link
ENCFF054SKC ENCFF054SKC.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 82.9 MB link
ENCFF089GNL ENCFF089GNL.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 72.4 MB link
ENCFF154EFX ENCFF154EFX.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 79.3 MB link
ENCFF168MQJ ENCFF168MQJ.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 65.6 MB link
ENCFF675PYM ENCFF675PYM.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 76.6 MB link
ENCFF256FBW ENCFF256FBW.fastq fastq (reads) reads 3.5 GB link
ENCFF528ELC ENCFF528ELC.fastq fastq (reads) reads 3.2 GB link
ENCFF693JKG ENCFF693JKG.fastq fastq (reads) reads 3.6 GB link
ENCFF907GMX ENCFF907GMX.fastq fastq (reads) reads 3.2 GB link
ENCFF344VKK ENCFF344VKK.tar tar (differential splicing quantifications); assembly: hg19; genome annotation: V19 differential splicing quantifications hg19 3.8 MB link
ENCFF755XVD ENCFF755XVD.tar tar (differential splicing quantifications); assembly: hg19; genome annotation: V19 differential splicing quantifications hg19 14.8 MB link
ENCFF947BVO ENCFF947BVO.tar tar (differential splicing quantifications); assembly: hg19; genome annotation: V19 differential splicing quantifications hg19 3.2 MB link
ENCFF003SFV ENCFF003SFV.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 5.6 MB link
ENCFF013AMG ENCFF013AMG.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 2.8 MB link
ENCFF175TRD ENCFF175TRD.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 1.9 MB link
ENCFF473NGX ENCFF473NGX.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 4.1 MB link
ENCFF934ZYX ENCFF934ZYX.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 1.8 MB link
ENCFF297OEK ENCFF297OEK.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V24 gene quantifications GRCh38 9.5 MB link
ENCFF911SNQ ENCFF911SNQ.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V24 gene quantifications GRCh38 9.5 MB link
ENCFF383NQU ENCFF383NQU.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V29 gene quantifications GRCh38 10.4 MB link
ENCFF605IAN ENCFF605IAN.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V29 gene quantifications GRCh38 10.4 MB link
ENCFF470RYI ENCFF470RYI.tsv tsv (gene quantifications); assembly: hg19; genome annotation: V19 gene quantifications hg19 9.1 MB link
ENCFF974AAP ENCFF974AAP.tsv tsv (gene quantifications); assembly: hg19; genome annotation: V19 gene quantifications hg19 9.1 MB link
ENCFF051FDT ENCFF051FDT.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V24 transcript quantifications GRCh38 25.4 MB link
ENCFF755NYE ENCFF755NYE.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V24 transcript quantifications GRCh38 25.4 MB link
ENCFF015JGR ENCFF015JGR.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 27.4 MB link
ENCFF335ZBB ENCFF335ZBB.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 27.3 MB link
ENCFF923HRY ENCFF923HRY.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 29.9 MB link
ENCFF936RMX ENCFF936RMX.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 29.9 MB link
ENCFF243PRK ENCFF243PRK.tsv tsv (transcript quantifications); assembly: hg19; genome annotation: V19 transcript quantifications hg19 25.0 MB link
ENCFF534YYI ENCFF534YYI.tsv tsv (transcript quantifications); assembly: hg19; genome annotation: V19 transcript quantifications hg19 25.0 MB link