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ENCSR577OVP

ENCSR ENCODE
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RNA-seq on K562 cells treated with an shRNA knockdown against DNAJC2. (DNAJC2_BGKLV24)

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

Summary

shRNA RNA-seq of DNAJC2 in Homo sapiens K562 expressing RNAi targeting H. sapiens DNAJC2

Overall Design

RNA-seq on K562 cells treated with an shRNA knockdown against DNAJC2. (DNAJC2_BGKLV24)

Analysis

View Data Processing
Analysis page is available for ENCSR577OVP.

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: 80.2 GB
Assay: shRNA RNA-seq
Target: DNAJC2
Biosample: Homo sapiens K562 expressing RNAi targeting H. sapiens DNAJC2
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
ENCFF324GVC ENCFF324GVC.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 3.7 GB link
ENCFF540NAB ENCFF540NAB.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 3.2 GB link
ENCFF555WBI ENCFF555WBI.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 3.1 GB link
ENCFF743XCK ENCFF743XCK.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 3.8 GB link
ENCFF574ZGJ ENCFF574ZGJ.bam bam (alignments); assembly: GRCh38; genome annotation: V29 alignments GRCh38 3.7 GB link
ENCFF923BAF ENCFF923BAF.bam bam (alignments); assembly: GRCh38; genome annotation: V29 alignments GRCh38 3.8 GB link
ENCFF246JPX ENCFF246JPX.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 3.1 GB link
ENCFF374URU ENCFF374URU.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 3.1 GB link
ENCFF531JNY ENCFF531JNY.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 3.7 GB link
ENCFF646BUZ ENCFF646BUZ.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 3.7 GB link
ENCFF862WEH ENCFF862WEH.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 3.2 GB link
ENCFF958ZED ENCFF958ZED.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 3.2 GB link
ENCFF296SLZ ENCFF296SLZ.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V24 transcriptome alignments GRCh38 4.3 GB link
ENCFF817HWU ENCFF817HWU.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V24 transcriptome alignments GRCh38 4.4 GB link
ENCFF200YDK ENCFF200YDK.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V29 transcriptome alignments GRCh38 4.8 GB link
ENCFF908LIP ENCFF908LIP.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V29 transcriptome alignments GRCh38 4.9 GB link
ENCFF361QWJ ENCFF361QWJ.bam bam (transcriptome alignments); assembly: hg19; genome annotation: V19 transcriptome alignments hg19 4.4 GB link
ENCFF880EJC ENCFF880EJC.bam bam (transcriptome alignments); assembly: hg19; genome annotation: V19 transcriptome alignments hg19 4.3 GB link
ENCFF232HFJ ENCFF232HFJ.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 78.1 MB link
ENCFF617JSW ENCFF617JSW.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 65.5 MB link
ENCFF633WFK ENCFF633WFK.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 68.9 MB link
ENCFF793LZE ENCFF793LZE.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 72.9 MB link
ENCFF545YNL ENCFF545YNL.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V29 minus strand signal of all reads GRCh38 72.9 MB link
ENCFF684JIB ENCFF684JIB.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V29 minus strand signal of all reads GRCh38 78.2 MB link
ENCFF032QZH ENCFF032QZH.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 72.5 MB link
ENCFF126YTV ENCFF126YTV.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 66.3 MB link
ENCFF582FAM ENCFF582FAM.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 66.3 MB link
ENCFF787NEK ENCFF787NEK.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 70.8 MB link
ENCFF864RHE ENCFF864RHE.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 77.2 MB link
ENCFF919APP ENCFF919APP.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 61.4 MB link
ENCFF124KMQ ENCFF124KMQ.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 60.9 MB link
ENCFF492MDX ENCFF492MDX.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 64.7 MB link
ENCFF908NSO ENCFF908NSO.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 68.9 MB link
ENCFF959GSB ENCFF959GSB.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 64.8 MB link
ENCFF326ZTS ENCFF326ZTS.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 minus strand signal of unique reads GRCh38 64.4 MB link
ENCFF664AOZ ENCFF664AOZ.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 minus strand signal of unique reads GRCh38 68.1 MB link
ENCFF052FEV ENCFF052FEV.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 60.3 MB link
ENCFF317NRP ENCFF317NRP.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 64.2 MB link
ENCFF399TLF ENCFF399TLF.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 64.7 MB link
ENCFF442ZLL ENCFF442ZLL.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 68.7 MB link
ENCFF621TMH ENCFF621TMH.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 56.5 MB link
ENCFF970OQP ENCFF970OQP.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 60.9 MB link
ENCFF169ZZA ENCFF169ZZA.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 66.2 MB link
ENCFF225BYJ ENCFF225BYJ.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 78.9 MB link
ENCFF382XXD ENCFF382XXD.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 69.5 MB link
ENCFF387TMS ENCFF387TMS.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 73.7 MB link
ENCFF165TRV ENCFF165TRV.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V29 plus strand signal of all reads GRCh38 78.9 MB link
ENCFF897YEV ENCFF897YEV.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V29 plus strand signal of all reads GRCh38 73.7 MB link
ENCFF324FMA ENCFF324FMA.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 62.5 MB link
ENCFF369SYQ ENCFF369SYQ.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 73.4 MB link
ENCFF377YHO ENCFF377YHO.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 67.4 MB link
ENCFF442GEW ENCFF442GEW.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 78.0 MB link
ENCFF803HQZ ENCFF803HQZ.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 67.4 MB link
ENCFF913WSA ENCFF913WSA.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 71.9 MB link
ENCFF429LQN ENCFF429LQN.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 62.1 MB link
ENCFF584FJY ENCFF584FJY.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 66.2 MB link
ENCFF623NBM ENCFF623NBM.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 70.3 MB link
ENCFF997KVV ENCFF997KVV.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 65.9 MB link
ENCFF202OHP ENCFF202OHP.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 plus strand signal of unique reads GRCh38 69.5 MB link
ENCFF626GBB ENCFF626GBB.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 plus strand signal of unique reads GRCh38 65.8 MB link
ENCFF451QSQ ENCFF451QSQ.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 65.7 MB link
ENCFF606FMU ENCFF606FMU.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 70.3 MB link
ENCFF653FFC ENCFF653FFC.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 58.0 MB link
ENCFF937JTS ENCFF937JTS.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 66.3 MB link
ENCFF942SGV ENCFF942SGV.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 61.8 MB link
ENCFF965XSR ENCFF965XSR.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 62.3 MB link
ENCFF202PQE ENCFF202PQE.fastq fastq (reads) reads 2.2 GB link
ENCFF509LZF ENCFF509LZF.fastq fastq (reads) reads 2.0 GB link
ENCFF572YPC ENCFF572YPC.fastq fastq (reads) reads 1.9 GB link
ENCFF945YQN ENCFF945YQN.fastq fastq (reads) reads 2.1 GB link
ENCFF092NAE ENCFF092NAE.tar tar (differential splicing quantifications); assembly: hg19; genome annotation: V19 differential splicing quantifications hg19 13.1 MB link
ENCFF621LMX ENCFF621LMX.tar tar (differential splicing quantifications); assembly: hg19; genome annotation: V19 differential splicing quantifications hg19 3.5 MB link
ENCFF851ZKJ ENCFF851ZKJ.tar tar (differential splicing quantifications); assembly: hg19; genome annotation: V19 differential splicing quantifications hg19 3.2 MB link
ENCFF241PCY ENCFF241PCY.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 4.1 MB link
ENCFF619XRO ENCFF619XRO.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 2.7 MB link
ENCFF766FRA ENCFF766FRA.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 1.8 MB link
ENCFF892CTK ENCFF892CTK.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 1.9 MB link
ENCFF892VAM ENCFF892VAM.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 5.6 MB link
ENCFF095NDS ENCFF095NDS.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V24 gene quantifications GRCh38 9.4 MB link
ENCFF714IFM ENCFF714IFM.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V24 gene quantifications GRCh38 9.4 MB link
ENCFF031GWD ENCFF031GWD.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V29 gene quantifications GRCh38 10.4 MB link
ENCFF505BEI ENCFF505BEI.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V29 gene quantifications GRCh38 10.4 MB link
ENCFF662GLZ ENCFF662GLZ.tsv tsv (gene quantifications); assembly: hg19; genome annotation: V19 gene quantifications hg19 9.1 MB link
ENCFF666OHO ENCFF666OHO.tsv tsv (gene quantifications); assembly: hg19; genome annotation: V19 gene quantifications hg19 9.1 MB link
ENCFF167IQA ENCFF167IQA.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V24 transcript quantifications GRCh38 25.3 MB link
ENCFF298NID ENCFF298NID.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V24 transcript quantifications GRCh38 25.3 MB link
ENCFF259BPS ENCFF259BPS.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 29.8 MB link
ENCFF316ONF ENCFF316ONF.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 27.3 MB link
ENCFF665WFU ENCFF665WFU.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 27.3 MB link
ENCFF715IRR ENCFF715IRR.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 29.8 MB link
ENCFF339XSR ENCFF339XSR.tsv tsv (transcript quantifications); assembly: hg19; genome annotation: V19 transcript quantifications hg19 24.9 MB link
ENCFF710HXU ENCFF710HXU.tsv tsv (transcript quantifications); assembly: hg19; genome annotation: V19 transcript quantifications hg19 24.9 MB link