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ENCSR048BWH

ENCSR ENCODE
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RNA-seq on K562 cells treated with an shRNA knockdown against HNRNPA1. (HNRNPA1_BGKLV21-B)

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

Summary

shRNA RNA-seq of HNRNPA1 in Homo sapiens K562 expressing RNAi targeting H. sapiens HNRNPA1

Overall Design

RNA-seq on K562 cells treated with an shRNA knockdown against HNRNPA1. (HNRNPA1_BGKLV21-B)

Analysis

View Data Processing
Analysis page is available for ENCSR048BWH.

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: 82.6 GB
Assay: shRNA RNA-seq
Target: HNRNPA1
Biosample: Homo sapiens K562 expressing RNAi targeting H. sapiens HNRNPA1
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
ENCFF033BYF ENCFF033BYF.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 3.7 GB link
ENCFF154NMI ENCFF154NMI.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 2.9 GB link
ENCFF167OCW ENCFF167OCW.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 4.0 GB link
ENCFF977BRY ENCFF977BRY.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 3.2 GB link
ENCFF512KPP ENCFF512KPP.bam bam (alignments); assembly: GRCh38; genome annotation: V29 alignments GRCh38 3.7 GB link
ENCFF587KMS ENCFF587KMS.bam bam (alignments); assembly: GRCh38; genome annotation: V29 alignments GRCh38 4.0 GB link
ENCFF191VLS ENCFF191VLS.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 3.1 GB link
ENCFF244AJP ENCFF244AJP.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 3.1 GB link
ENCFF395AZN ENCFF395AZN.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 2.8 GB link
ENCFF398HLD ENCFF398HLD.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 3.5 GB link
ENCFF693BLE ENCFF693BLE.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 2.8 GB link
ENCFF979PHM ENCFF979PHM.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 3.8 GB link
ENCFF699HPM ENCFF699HPM.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V24 transcriptome alignments GRCh38 4.9 GB link
ENCFF790QVN ENCFF790QVN.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V24 transcriptome alignments GRCh38 4.5 GB link
ENCFF249JMN ENCFF249JMN.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V29 transcriptome alignments GRCh38 5.6 GB link
ENCFF967CMR ENCFF967CMR.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V29 transcriptome alignments GRCh38 5.1 GB link
ENCFF177CJU ENCFF177CJU.bam bam (transcriptome alignments); assembly: hg19; genome annotation: V19 transcriptome alignments hg19 4.4 GB link
ENCFF304EBE ENCFF304EBE.bam bam (transcriptome alignments); assembly: hg19; genome annotation: V19 transcriptome alignments hg19 4.8 GB link
ENCFF332QYC ENCFF332QYC.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 100.5 MB link
ENCFF333VNG ENCFF333VNG.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 97.1 MB link
ENCFF661EVY ENCFF661EVY.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 87.0 MB link
ENCFF889OON ENCFF889OON.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 89.5 MB link
ENCFF866NEP ENCFF866NEP.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V29 minus strand signal of all reads GRCh38 100.5 MB link
ENCFF986SQY ENCFF986SQY.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V29 minus strand signal of all reads GRCh38 97.1 MB link
ENCFF344WWQ ENCFF344WWQ.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 88.6 MB link
ENCFF459AYH ENCFF459AYH.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 91.9 MB link
ENCFF607KKJ ENCFF607KKJ.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 96.9 MB link
ENCFF725WIK ENCFF725WIK.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 87.0 MB link
ENCFF909SCU ENCFF909SCU.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 84.4 MB link
ENCFF923RBC ENCFF923RBC.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 99.8 MB link
ENCFF114HON ENCFF114HON.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 81.5 MB link
ENCFF142NTX ENCFF142NTX.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 83.6 MB link
ENCFF606MNK ENCFF606MNK.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 85.7 MB link
ENCFF943CBB ENCFF943CBB.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 88.4 MB link
ENCFF520IPH ENCFF520IPH.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 minus strand signal of unique reads GRCh38 88.9 MB link
ENCFF829UJA ENCFF829UJA.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 minus strand signal of unique reads GRCh38 86.4 MB link
ENCFF042IYS ENCFF042IYS.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 88.8 MB link
ENCFF203UTM ENCFF203UTM.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 82.8 MB link
ENCFF289FQB ENCFF289FQB.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 86.3 MB link
ENCFF435KAR ENCFF435KAR.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 76.3 MB link
ENCFF713RWO ENCFF713RWO.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 80.1 MB link
ENCFF715SRR ENCFF715SRR.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 81.8 MB link
ENCFF031MZA ENCFF031MZA.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 101.6 MB link
ENCFF035TEK ENCFF035TEK.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 98.1 MB link
ENCFF358ZTE ENCFF358ZTE.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 88.0 MB link
ENCFF586TCG ENCFF586TCG.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 90.5 MB link
ENCFF277LDM ENCFF277LDM.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V29 plus strand signal of all reads GRCh38 98.1 MB link
ENCFF751JET ENCFF751JET.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V29 plus strand signal of all reads GRCh38 101.6 MB link
ENCFF496BBZ ENCFF496BBZ.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 97.9 MB link
ENCFF498RVE ENCFF498RVE.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 85.7 MB link
ENCFF611DVB ENCFF611DVB.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 93.4 MB link
ENCFF716AUE ENCFF716AUE.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 100.9 MB link
ENCFF808GCZ ENCFF808GCZ.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 88.5 MB link
ENCFF943AHU ENCFF943AHU.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 90.0 MB link
ENCFF130JLY ENCFF130JLY.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 85.3 MB link
ENCFF253EBY ENCFF253EBY.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 90.4 MB link
ENCFF334EGN ENCFF334EGN.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 87.5 MB link
ENCFF492FVK ENCFF492FVK.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 83.2 MB link
ENCFF132TJO ENCFF132TJO.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 plus strand signal of unique reads GRCh38 88.2 MB link
ENCFF817OCS ENCFF817OCS.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 plus strand signal of unique reads GRCh38 90.8 MB link
ENCFF085XAE ENCFF085XAE.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 84.8 MB link
ENCFF303QZW ENCFF303QZW.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 78.2 MB link
ENCFF488SKB ENCFF488SKB.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 83.8 MB link
ENCFF533KGF ENCFF533KGF.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 90.9 MB link
ENCFF860QDY ENCFF860QDY.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 88.3 MB link
ENCFF933GDS ENCFF933GDS.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 82.2 MB link
ENCFF015PIM ENCFF015PIM.fastq fastq (reads) reads 2.1 GB link
ENCFF711RAQ ENCFF711RAQ.fastq fastq (reads) reads 2.0 GB link
ENCFF893RDF ENCFF893RDF.fastq fastq (reads) reads 1.9 GB link
ENCFF997NCB ENCFF997NCB.fastq fastq (reads) reads 2.2 GB link
ENCFF258VNP ENCFF258VNP.tar tar (differential splicing quantifications); assembly: hg19; genome annotation: V19 differential splicing quantifications hg19 4.7 MB link
ENCFF611RFN ENCFF611RFN.tar tar (differential splicing quantifications); assembly: hg19; genome annotation: V19 differential splicing quantifications hg19 3.9 MB link
ENCFF738LPL ENCFF738LPL.tar tar (differential splicing quantifications); assembly: hg19; genome annotation: V19 differential splicing quantifications hg19 16.7 MB link
ENCFF035ABY ENCFF035ABY.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 1.7 MB link
ENCFF414BHG ENCFF414BHG.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 2.9 MB link
ENCFF447RXL ENCFF447RXL.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 4.4 MB link
ENCFF540QSJ ENCFF540QSJ.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 5.6 MB link
ENCFF693BLK ENCFF693BLK.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 1.9 MB link
ENCFF239OGJ ENCFF239OGJ.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V24 gene quantifications GRCh38 9.5 MB link
ENCFF864FLD ENCFF864FLD.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V24 gene quantifications GRCh38 9.4 MB link
ENCFF210OYV ENCFF210OYV.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V29 gene quantifications GRCh38 10.4 MB link
ENCFF242NXX ENCFF242NXX.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V29 gene quantifications GRCh38 10.4 MB link
ENCFF733NQV ENCFF733NQV.tsv tsv (gene quantifications); assembly: hg19; genome annotation: V19 gene quantifications hg19 9.1 MB link
ENCFF859JEW ENCFF859JEW.tsv tsv (gene quantifications); assembly: hg19; genome annotation: V19 gene quantifications hg19 9.1 MB link
ENCFF879LRP ENCFF879LRP.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V24 transcript quantifications GRCh38 25.3 MB link
ENCFF892ONO ENCFF892ONO.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V24 transcript quantifications GRCh38 25.3 MB link
ENCFF070ZTT ENCFF070ZTT.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 27.4 MB link
ENCFF213COD ENCFF213COD.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 27.4 MB link
ENCFF575EGY ENCFF575EGY.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 29.8 MB link
ENCFF818HGM ENCFF818HGM.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 29.8 MB link
ENCFF130YGS ENCFF130YGS.tsv tsv (transcript quantifications); assembly: hg19; genome annotation: V19 transcript quantifications hg19 24.9 MB link
ENCFF364WMW ENCFF364WMW.tsv tsv (transcript quantifications); assembly: hg19; genome annotation: V19 transcript quantifications hg19 24.9 MB link