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ENCSR844QNT

ENCSR ENCODE
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RNA-seq on K562 cells treated with an shRNA knockdown against PPP1R8. (PPP1R8_BGKLV28)

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

Summary

shRNA RNA-seq of PPP1R8 in Homo sapiens K562 expressing RNAi targeting H. sapiens PPP1R8

Overall Design

RNA-seq on K562 cells treated with an shRNA knockdown against PPP1R8. (PPP1R8_BGKLV28)

Analysis

View Data Processing
Analysis page is available for ENCSR844QNT.

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: 126.3 GB
Assay: shRNA RNA-seq
Target: PPP1R8
Biosample: Homo sapiens K562 expressing RNAi targeting H. sapiens PPP1R8
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
ENCFF295CFK ENCFF295CFK.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 6.6 GB link
ENCFF472UYI ENCFF472UYI.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 5.4 GB link
ENCFF677ZIS ENCFF677ZIS.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 4.3 GB link
ENCFF933YGM ENCFF933YGM.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 5.3 GB link
ENCFF202PRN ENCFF202PRN.bam bam (alignments); assembly: GRCh38; genome annotation: V29 alignments GRCh38 5.3 GB link
ENCFF339WFX ENCFF339WFX.bam bam (alignments); assembly: GRCh38; genome annotation: V29 alignments GRCh38 6.6 GB link
ENCFF253YBH ENCFF253YBH.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 4.2 GB link
ENCFF583PFG ENCFF583PFG.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 5.3 GB link
ENCFF743GFT ENCFF743GFT.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 5.3 GB link
ENCFF820FCI ENCFF820FCI.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 6.4 GB link
ENCFF900YPJ ENCFF900YPJ.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 5.1 GB link
ENCFF902AHB ENCFF902AHB.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 4.2 GB link
ENCFF574OPN ENCFF574OPN.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V24 transcriptome alignments GRCh38 7.9 GB link
ENCFF622XFZ ENCFF622XFZ.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V24 transcriptome alignments GRCh38 6.3 GB link
ENCFF074GEM ENCFF074GEM.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V29 transcriptome alignments GRCh38 9.0 GB link
ENCFF112LDS ENCFF112LDS.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V29 transcriptome alignments GRCh38 7.2 GB link
ENCFF050YDG ENCFF050YDG.bam bam (transcriptome alignments); assembly: hg19; genome annotation: V19 transcriptome alignments hg19 7.9 GB link
ENCFF812WMW ENCFF812WMW.bam bam (transcriptome alignments); assembly: hg19; genome annotation: V19 transcriptome alignments hg19 6.3 GB link
ENCFF309XUM ENCFF309XUM.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 109.6 MB link
ENCFF520LTW ENCFF520LTW.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 84.7 MB link
ENCFF619TPN ENCFF619TPN.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 96.9 MB link
ENCFF848HPJ ENCFF848HPJ.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 97.0 MB link
ENCFF576PSL ENCFF576PSL.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V29 minus strand signal of all reads GRCh38 97.1 MB link
ENCFF959CYF ENCFF959CYF.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V29 minus strand signal of all reads GRCh38 109.3 MB link
ENCFF010GOR ENCFF010GOR.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 95.6 MB link
ENCFF068GZB ENCFF068GZB.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 108.5 MB link
ENCFF315XLK ENCFF315XLK.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 99.1 MB link
ENCFF375BSU ENCFF375BSU.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 95.6 MB link
ENCFF586KQE ENCFF586KQE.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 83.1 MB link
ENCFF954KQK ENCFF954KQK.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 87.2 MB link
ENCFF190TSC ENCFF190TSC.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 78.7 MB link
ENCFF233CWA ENCFF233CWA.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 90.1 MB link
ENCFF308KKN ENCFF308KKN.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 97.4 MB link
ENCFF727DHK ENCFF727DHK.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 84.6 MB link
ENCFF165BUG ENCFF165BUG.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 minus strand signal of unique reads GRCh38 85.5 MB link
ENCFF338FCZ ENCFF338FCZ.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 minus strand signal of unique reads GRCh38 97.3 MB link
ENCFF072CKB ENCFF072CKB.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 76.6 MB link
ENCFF121FQN ENCFF121FQN.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 97.0 MB link
ENCFF310GRL ENCFF310GRL.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 79.3 MB link
ENCFF794RRI ENCFF794RRI.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 85.2 MB link
ENCFF958WFO ENCFF958WFO.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 87.4 MB link
ENCFF980LKA ENCFF980LKA.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 90.6 MB link
ENCFF401WBM ENCFF401WBM.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 98.6 MB link
ENCFF459VSO ENCFF459VSO.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 111.4 MB link
ENCFF474TKZ ENCFF474TKZ.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 86.1 MB link
ENCFF964PID ENCFF964PID.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 98.6 MB link
ENCFF121YRO ENCFF121YRO.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V29 plus strand signal of all reads GRCh38 111.1 MB link
ENCFF685QOK ENCFF685QOK.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V29 plus strand signal of all reads GRCh38 98.6 MB link
ENCFF129LMH ENCFF129LMH.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 97.9 MB link
ENCFF501CCV ENCFF501CCV.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 110.5 MB link
ENCFF679ENN ENCFF679ENN.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 101.3 MB link
ENCFF722AML ENCFF722AML.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 85.0 MB link
ENCFF874URN ENCFF874URN.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 97.3 MB link
ENCFF983WRC ENCFF983WRC.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 89.2 MB link
ENCFF162RWU ENCFF162RWU.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 92.3 MB link
ENCFF205XRN ENCFF205XRN.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 86.8 MB link
ENCFF546IKF ENCFF546IKF.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 99.9 MB link
ENCFF987LEF ENCFF987LEF.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 80.7 MB link
ENCFF229RJC ENCFF229RJC.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 plus strand signal of unique reads GRCh38 87.7 MB link
ENCFF972VCX ENCFF972VCX.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 plus strand signal of unique reads GRCh38 99.8 MB link
ENCFF065IGH ENCFF065IGH.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 81.7 MB link
ENCFF100BUG ENCFF100BUG.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 79.0 MB link
ENCFF222HKJ ENCFF222HKJ.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 93.2 MB link
ENCFF286KKI ENCFF286KKI.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 90.0 MB link
ENCFF509CFM ENCFF509CFM.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 87.7 MB link
ENCFF906ITO ENCFF906ITO.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 99.9 MB link
ENCFF191JPS ENCFF191JPS.fastq fastq (reads) reads 3.7 GB link
ENCFF539KOW ENCFF539KOW.fastq fastq (reads) reads 2.9 GB link
ENCFF903WCH ENCFF903WCH.fastq fastq (reads) reads 2.9 GB link
ENCFF964YSU ENCFF964YSU.fastq fastq (reads) reads 3.7 GB link
ENCFF043SFD ENCFF043SFD.tar tar (differential splicing quantifications); assembly: hg19; genome annotation: V19 differential splicing quantifications hg19 3.9 MB link
ENCFF499WPA ENCFF499WPA.tar tar (differential splicing quantifications); assembly: hg19; genome annotation: V19 differential splicing quantifications hg19 16.3 MB link
ENCFF851KQP ENCFF851KQP.tar tar (differential splicing quantifications); assembly: hg19; genome annotation: V19 differential splicing quantifications hg19 5.1 MB link
ENCFF247DTZ ENCFF247DTZ.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 4.3 MB link
ENCFF700VIX ENCFF700VIX.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 2.0 MB link
ENCFF835BVA ENCFF835BVA.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 2.9 MB link
ENCFF847PDS ENCFF847PDS.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 5.6 MB link
ENCFF953DWU ENCFF953DWU.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 1.6 MB link
ENCFF557LLU ENCFF557LLU.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V24 gene quantifications GRCh38 9.5 MB link
ENCFF662WGJ ENCFF662WGJ.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V24 gene quantifications GRCh38 9.5 MB link
ENCFF352MYR ENCFF352MYR.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V29 gene quantifications GRCh38 10.4 MB link
ENCFF580JGE ENCFF580JGE.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V29 gene quantifications GRCh38 10.4 MB link
ENCFF640HHS ENCFF640HHS.tsv tsv (gene quantifications); assembly: hg19; genome annotation: V19 gene quantifications hg19 9.1 MB link
ENCFF826FLR ENCFF826FLR.tsv tsv (gene quantifications); assembly: hg19; genome annotation: V19 gene quantifications hg19 9.1 MB link
ENCFF061PZP ENCFF061PZP.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V24 transcript quantifications GRCh38 25.4 MB link
ENCFF723QIE ENCFF723QIE.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V24 transcript quantifications GRCh38 25.4 MB link
ENCFF120OGL ENCFF120OGL.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 27.4 MB link
ENCFF403NSJ ENCFF403NSJ.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 29.9 MB link
ENCFF788RLU ENCFF788RLU.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 29.9 MB link
ENCFF979FTI ENCFF979FTI.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 27.4 MB link
ENCFF385YUD ENCFF385YUD.tsv tsv (transcript quantifications); assembly: hg19; genome annotation: V19 transcript quantifications hg19 24.9 MB link
ENCFF819LSM ENCFF819LSM.tsv tsv (transcript quantifications); assembly: hg19; genome annotation: V19 transcript quantifications hg19 25.0 MB link