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ENCSR416ZJH

ENCSR ENCODE
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RNA-seq on K562 cells treated with an shRNA knockdown against PABPN1. (PABPN1_BGKLV28)

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

Summary

shRNA RNA-seq of PABPN1 in Homo sapiens K562 expressing RNAi targeting H. sapiens PABPN1

Overall Design

RNA-seq on K562 cells treated with an shRNA knockdown against PABPN1. (PABPN1_BGKLV28)

Analysis

View Data Processing
Analysis page is available for ENCSR416ZJH.

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: 103.1 GB
Assay: shRNA RNA-seq
Target: PABPN1
Biosample: Homo sapiens K562 expressing RNAi targeting H. sapiens PABPN1
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
ENCFF035QOQ ENCFF035QOQ.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 5.8 GB link
ENCFF277KIW ENCFF277KIW.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 4.5 GB link
ENCFF311ESK ENCFF311ESK.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 4.7 GB link
ENCFF403ZRW ENCFF403ZRW.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 3.8 GB link
ENCFF305KZP ENCFF305KZP.bam bam (alignments); assembly: GRCh38; genome annotation: V29 alignments GRCh38 4.7 GB link
ENCFF451NNK ENCFF451NNK.bam bam (alignments); assembly: GRCh38; genome annotation: V29 alignments GRCh38 5.8 GB link
ENCFF101MSD ENCFF101MSD.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 3.8 GB link
ENCFF173EOE ENCFF173EOE.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 3.9 GB link
ENCFF185PSI ENCFF185PSI.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 3.9 GB link
ENCFF214TTT ENCFF214TTT.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 3.8 GB link
ENCFF423ESU ENCFF423ESU.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 4.6 GB link
ENCFF632EIZ ENCFF632EIZ.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 4.7 GB link
ENCFF434JBV ENCFF434JBV.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V24 transcriptome alignments GRCh38 5.5 GB link
ENCFF484SBW ENCFF484SBW.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V24 transcriptome alignments GRCh38 5.5 GB link
ENCFF331VML ENCFF331VML.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V29 transcriptome alignments GRCh38 6.3 GB link
ENCFF979IHR ENCFF979IHR.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V29 transcriptome alignments GRCh38 6.2 GB link
ENCFF170WTB ENCFF170WTB.bam bam (transcriptome alignments); assembly: hg19; genome annotation: V19 transcriptome alignments hg19 5.5 GB link
ENCFF570SAQ ENCFF570SAQ.bam bam (transcriptome alignments); assembly: hg19; genome annotation: V19 transcriptome alignments hg19 5.5 GB link
ENCFF068JRX ENCFF068JRX.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 91.2 MB link
ENCFF085KUJ ENCFF085KUJ.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 80.5 MB link
ENCFF347DVM ENCFF347DVM.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 87.6 MB link
ENCFF355CYI ENCFF355CYI.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 77.6 MB link
ENCFF496SNC ENCFF496SNC.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V29 minus strand signal of all reads GRCh38 87.6 MB link
ENCFF738MZJ ENCFF738MZJ.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V29 minus strand signal of all reads GRCh38 91.2 MB link
ENCFF122UIQ ENCFF122UIQ.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 86.8 MB link
ENCFF152ZBQ ENCFF152ZBQ.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 89.2 MB link
ENCFF179YZU ENCFF179YZU.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 77.0 MB link
ENCFF518HVG ENCFF518HVG.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 79.2 MB link
ENCFF792PKI ENCFF792PKI.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 82.2 MB link
ENCFF834YQO ENCFF834YQO.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 75.4 MB link
ENCFF223YVI ENCFF223YVI.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 71.7 MB link
ENCFF227INW ENCFF227INW.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 79.9 MB link
ENCFF599MZW ENCFF599MZW.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 74.2 MB link
ENCFF775IFS ENCFF775IFS.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 77.8 MB link
ENCFF362LAP ENCFF362LAP.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 minus strand signal of unique reads GRCh38 80.7 MB link
ENCFF873EKK ENCFF873EKK.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 minus strand signal of unique reads GRCh38 78.1 MB link
ENCFF175IDX ENCFF175IDX.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 75.5 MB link
ENCFF190HTP ENCFF190HTP.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 80.4 MB link
ENCFF354GKT ENCFF354GKT.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 73.0 MB link
ENCFF387IFO ENCFF387IFO.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 69.6 MB link
ENCFF420GMS ENCFF420GMS.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 77.5 MB link
ENCFF861UPR ENCFF861UPR.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 70.8 MB link
ENCFF120PYL ENCFF120PYL.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 89.5 MB link
ENCFF158XWA ENCFF158XWA.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 79.3 MB link
ENCFF477PDO ENCFF477PDO.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 93.0 MB link
ENCFF696AUC ENCFF696AUC.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 82.1 MB link
ENCFF574KNF ENCFF574KNF.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V29 plus strand signal of all reads GRCh38 89.4 MB link
ENCFF914PFQ ENCFF914PFQ.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V29 plus strand signal of all reads GRCh38 93.1 MB link
ENCFF070WLK ENCFF070WLK.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 81.3 MB link
ENCFF098MKW ENCFF098MKW.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 88.7 MB link
ENCFF154EML ENCFF154EML.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 79.0 MB link
ENCFF327CAL ENCFF327CAL.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 84.2 MB link
ENCFF511IOG ENCFF511IOG.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 91.1 MB link
ENCFF841OAL ENCFF841OAL.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 77.5 MB link
ENCFF111TGX ENCFF111TGX.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 76.2 MB link
ENCFF415JSQ ENCFF415JSQ.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 82.2 MB link
ENCFF741XGR ENCFF741XGR.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 73.7 MB link
ENCFF914OZW ENCFF914OZW.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 80.2 MB link
ENCFF304AJG ENCFF304AJG.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 plus strand signal of unique reads GRCh38 80.5 MB link
ENCFF312JER ENCFF312JER.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 plus strand signal of unique reads GRCh38 83.0 MB link
ENCFF273ZCQ ENCFF273ZCQ.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 72.1 MB link
ENCFF449AJS ENCFF449AJS.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 82.9 MB link
ENCFF476GSK ENCFF476GSK.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 77.8 MB link
ENCFF535TRM ENCFF535TRM.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 80.1 MB link
ENCFF927MSB ENCFF927MSB.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 73.2 MB link
ENCFF944QEW ENCFF944QEW.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 75.4 MB link
ENCFF018JDZ ENCFF018JDZ.fastq fastq (reads) reads 2.7 GB link
ENCFF273CYL ENCFF273CYL.fastq fastq (reads) reads 2.7 GB link
ENCFF616PSW ENCFF616PSW.fastq fastq (reads) reads 2.6 GB link
ENCFF687PZS ENCFF687PZS.fastq fastq (reads) reads 2.6 GB link
ENCFF411XGX ENCFF411XGX.tar tar (differential splicing quantifications); assembly: hg19; genome annotation: V19 differential splicing quantifications hg19 4.8 MB link
ENCFF792FAV ENCFF792FAV.tar tar (differential splicing quantifications); assembly: hg19; genome annotation: V19 differential splicing quantifications hg19 15.2 MB link
ENCFF925YEN ENCFF925YEN.tar tar (differential splicing quantifications); assembly: hg19; genome annotation: V19 differential splicing quantifications hg19 3.6 MB link
ENCFF079NNW ENCFF079NNW.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 3.0 MB link
ENCFF129URO ENCFF129URO.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 1.7 MB link
ENCFF160PKJ ENCFF160PKJ.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 1.9 MB link
ENCFF599ZAM ENCFF599ZAM.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 4.3 MB link
ENCFF881GMG ENCFF881GMG.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 5.6 MB link
ENCFF589VDQ ENCFF589VDQ.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V24 gene quantifications GRCh38 9.5 MB link
ENCFF827QLY ENCFF827QLY.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V24 gene quantifications GRCh38 9.5 MB link
ENCFF134BDB ENCFF134BDB.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V29 gene quantifications GRCh38 10.4 MB link
ENCFF858WKG ENCFF858WKG.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V29 gene quantifications GRCh38 10.4 MB link
ENCFF574WHT ENCFF574WHT.tsv tsv (gene quantifications); assembly: hg19; genome annotation: V19 gene quantifications hg19 9.1 MB link
ENCFF875HVD ENCFF875HVD.tsv tsv (gene quantifications); assembly: hg19; genome annotation: V19 gene quantifications hg19 9.1 MB link
ENCFF122KQZ ENCFF122KQZ.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V24 transcript quantifications GRCh38 25.3 MB link
ENCFF798OZU ENCFF798OZU.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V24 transcript quantifications GRCh38 25.4 MB link
ENCFF234VDD ENCFF234VDD.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 29.9 MB link
ENCFF346JPC ENCFF346JPC.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 27.4 MB link
ENCFF605EDD ENCFF605EDD.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 29.8 MB link
ENCFF946YED ENCFF946YED.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 27.4 MB link
ENCFF753VRV ENCFF753VRV.tsv tsv (transcript quantifications); assembly: hg19; genome annotation: V19 transcript quantifications hg19 24.9 MB link
ENCFF759EGU ENCFF759EGU.tsv tsv (transcript quantifications); assembly: hg19; genome annotation: V19 transcript quantifications hg19 24.9 MB link