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ENCSR330KHN

ENCSR ENCODE
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RNA-seq on HepG2 cells treated with an shRNA knockdown against RBM22. (RBM22_BGHLV37)

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

Summary

shRNA RNA-seq of RBM22 in Homo sapiens HepG2 expressing RNAi targeting H. sapiens RBM22

Overall Design

RNA-seq on HepG2 cells treated with an shRNA knockdown against RBM22. (RBM22_BGHLV37)

Analysis

View Data Processing
Analysis page is available for ENCSR330KHN.

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: 104.3 GB
Assay: shRNA RNA-seq
Target: RBM22
Biosample: Homo sapiens HepG2 expressing RNAi targeting H. sapiens RBM22
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
ENCFF051INT ENCFF051INT.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 4.7 GB link
ENCFF557HSG ENCFF557HSG.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 4.1 GB link
ENCFF608RJT ENCFF608RJT.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 5.9 GB link
ENCFF905OMV ENCFF905OMV.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 3.3 GB link
ENCFF034EKP ENCFF034EKP.bam bam (alignments); assembly: GRCh38; genome annotation: V29 alignments GRCh38 5.9 GB link
ENCFF768VAQ ENCFF768VAQ.bam bam (alignments); assembly: GRCh38; genome annotation: V29 alignments GRCh38 4.1 GB link
ENCFF030OLZ ENCFF030OLZ.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 5.4 GB link
ENCFF369NEZ ENCFF369NEZ.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 3.9 GB link
ENCFF475XDR ENCFF475XDR.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 3.2 GB link
ENCFF776RHY ENCFF776RHY.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 4.5 GB link
ENCFF778TZK ENCFF778TZK.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 3.2 GB link
ENCFF991DPE ENCFF991DPE.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 4.5 GB link
ENCFF465QTD ENCFF465QTD.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V24 transcriptome alignments GRCh38 4.8 GB link
ENCFF891ULQ ENCFF891ULQ.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V24 transcriptome alignments GRCh38 6.6 GB link
ENCFF047KDX ENCFF047KDX.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V29 transcriptome alignments GRCh38 7.5 GB link
ENCFF064YRF ENCFF064YRF.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V29 transcriptome alignments GRCh38 5.5 GB link
ENCFF225UCU ENCFF225UCU.bam bam (transcriptome alignments); assembly: hg19; genome annotation: V19 transcriptome alignments hg19 6.5 GB link
ENCFF675OWS ENCFF675OWS.bam bam (transcriptome alignments); assembly: hg19; genome annotation: V19 transcriptome alignments hg19 4.8 GB link
ENCFF059MHG ENCFF059MHG.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 113.2 MB link
ENCFF281MXR ENCFF281MXR.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 125.4 MB link
ENCFF551YSY ENCFF551YSY.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 92.2 MB link
ENCFF735TME ENCFF735TME.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 102.9 MB link
ENCFF228YIY ENCFF228YIY.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V29 minus strand signal of all reads GRCh38 102.9 MB link
ENCFF885CHG ENCFF885CHG.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V29 minus strand signal of all reads GRCh38 125.5 MB link
ENCFF129YYF ENCFF129YYF.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 109.6 MB link
ENCFF296VXO ENCFF296VXO.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 122.7 MB link
ENCFF444HUW ENCFF444HUW.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 114.4 MB link
ENCFF657HAH ENCFF657HAH.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 89.6 MB link
ENCFF729XTQ ENCFF729XTQ.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 102.3 MB link
ENCFF830YJW ENCFF830YJW.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 95.1 MB link
ENCFF438SLU ENCFF438SLU.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 104.7 MB link
ENCFF472TON ENCFF472TON.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 92.0 MB link
ENCFF651VGX ENCFF651VGX.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 85.7 MB link
ENCFF652KVG ENCFF652KVG.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 111.2 MB link
ENCFF829UZA ENCFF829UZA.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 minus strand signal of unique reads GRCh38 92.0 MB link
ENCFF848GTK ENCFF848GTK.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 minus strand signal of unique reads GRCh38 110.7 MB link
ENCFF037ALK ENCFF037ALK.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 101.2 MB link
ENCFF057MTL ENCFF057MTL.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 86.3 MB link
ENCFF175ZDU ENCFF175ZDU.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 111.0 MB link
ENCFF207VZI ENCFF207VZI.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 105.5 MB link
ENCFF803UKG ENCFF803UKG.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 91.6 MB link
ENCFF925AQH ENCFF925AQH.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 82.1 MB link
ENCFF093UUV ENCFF093UUV.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 94.3 MB link
ENCFF116KTR ENCFF116KTR.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 128.3 MB link
ENCFF664VTL ENCFF664VTL.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 115.9 MB link
ENCFF785LQT ENCFF785LQT.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 105.1 MB link
ENCFF350RIC ENCFF350RIC.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V29 plus strand signal of all reads GRCh38 128.3 MB link
ENCFF670LAF ENCFF670LAF.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V29 plus strand signal of all reads GRCh38 105.1 MB link
ENCFF027TTR ENCFF027TTR.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 104.2 MB link
ENCFF183RZB ENCFF183RZB.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 97.4 MB link
ENCFF322GOD ENCFF322GOD.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 112.2 MB link
ENCFF527RQI ENCFF527RQI.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 91.7 MB link
ENCFF676DPD ENCFF676DPD.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 125.2 MB link
ENCFF963QGU ENCFF963QGU.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 117.3 MB link
ENCFF472GOP ENCFF472GOP.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 95.0 MB link
ENCFF889UQA ENCFF889UQA.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 108.2 MB link
ENCFF927ZBN ENCFF927ZBN.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 115.1 MB link
ENCFF958PTR ENCFF958PTR.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 88.4 MB link
ENCFF060GDE ENCFF060GDE.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 plus strand signal of unique reads GRCh38 95.0 MB link
ENCFF452UTT ENCFF452UTT.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 plus strand signal of unique reads GRCh38 114.6 MB link
ENCFF049MMN ENCFF049MMN.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 104.7 MB link
ENCFF218FQG ENCFF218FQG.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 89.1 MB link
ENCFF399VHL ENCFF399VHL.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 84.7 MB link
ENCFF486XZL ENCFF486XZL.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 94.4 MB link
ENCFF830GFR ENCFF830GFR.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 114.8 MB link
ENCFF853SPZ ENCFF853SPZ.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 109.1 MB link
ENCFF103BIV ENCFF103BIV.fastq fastq (reads) reads 2.2 GB link
ENCFF144WRK ENCFF144WRK.fastq fastq (reads) reads 3.1 GB link
ENCFF495USF ENCFF495USF.fastq fastq (reads) reads 3.0 GB link
ENCFF986CJT ENCFF986CJT.fastq fastq (reads) reads 2.2 GB link
ENCFF532VWT ENCFF532VWT.tar tar (differential splicing quantifications); assembly: hg19; genome annotation: V19 differential splicing quantifications hg19 5.4 MB link
ENCFF640VCX ENCFF640VCX.tar tar (differential splicing quantifications); assembly: hg19; genome annotation: V19 differential splicing quantifications hg19 18.3 MB link
ENCFF823OOV ENCFF823OOV.tar tar (differential splicing quantifications); assembly: hg19; genome annotation: V19 differential splicing quantifications hg19 4.0 MB link
ENCFF026PKC ENCFF026PKC.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 3.0 MB link
ENCFF226VJI ENCFF226VJI.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 2.0 MB link
ENCFF307JNO ENCFF307JNO.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 5.6 MB link
ENCFF631PIK ENCFF631PIK.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 1.7 MB link
ENCFF768GAH ENCFF768GAH.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 4.6 MB link
ENCFF131FUZ ENCFF131FUZ.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V24 gene quantifications GRCh38 9.4 MB link
ENCFF580ZYM ENCFF580ZYM.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V24 gene quantifications GRCh38 9.5 MB link
ENCFF038EHT ENCFF038EHT.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V29 gene quantifications GRCh38 10.4 MB link
ENCFF427AZY ENCFF427AZY.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V29 gene quantifications GRCh38 10.4 MB link
ENCFF418ZTW ENCFF418ZTW.tsv tsv (gene quantifications); assembly: hg19; genome annotation: V19 gene quantifications hg19 9.1 MB link
ENCFF965ZCJ ENCFF965ZCJ.tsv tsv (gene quantifications); assembly: hg19; genome annotation: V19 gene quantifications hg19 9.1 MB link
ENCFF291NKP ENCFF291NKP.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V24 transcript quantifications GRCh38 25.3 MB link
ENCFF657PCX ENCFF657PCX.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V24 transcript quantifications GRCh38 25.3 MB link
ENCFF246AKQ ENCFF246AKQ.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 29.8 MB link
ENCFF409BOE ENCFF409BOE.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 29.8 MB link
ENCFF411VKL ENCFF411VKL.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 27.4 MB link
ENCFF524JJT ENCFF524JJT.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 27.5 MB link
ENCFF165GUZ ENCFF165GUZ.tsv tsv (transcript quantifications); assembly: hg19; genome annotation: V19 transcript quantifications hg19 24.9 MB link
ENCFF390UJF ENCFF390UJF.tsv tsv (transcript quantifications); assembly: hg19; genome annotation: V19 transcript quantifications hg19 24.9 MB link