← All datasets

ENCSR341PZW

ENCSR ENCODE
Export SRA CSV View on ENCODE

RNA-seq on K562 cells treated with an shRNA knockdown against WDR43. (WDR43_BGKLV34)

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

Summary

shRNA RNA-seq of WDR43 in Homo sapiens K562 expressing RNAi targeting H. sapiens WDR43

Overall Design

RNA-seq on K562 cells treated with an shRNA knockdown against WDR43. (WDR43_BGKLV34)

Analysis

View Data Processing
Analysis page is available for ENCSR341PZW.

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: 117.1 GB
Assay: shRNA RNA-seq
Target: WDR43
Biosample: Homo sapiens K562 expressing RNAi targeting H. sapiens WDR43
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
ENCFF047KHQ ENCFF047KHQ.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 4.6 GB link
ENCFF752MBC ENCFF752MBC.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 5.6 GB link
ENCFF770CEF ENCFF770CEF.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 4.6 GB link
ENCFF876NAI ENCFF876NAI.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 5.6 GB link
ENCFF277EQW ENCFF277EQW.bam bam (alignments); assembly: GRCh38; genome annotation: V29 alignments GRCh38 5.6 GB link
ENCFF441QBT ENCFF441QBT.bam bam (alignments); assembly: GRCh38; genome annotation: V29 alignments GRCh38 5.6 GB link
ENCFF141NGN ENCFF141NGN.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 4.5 GB link
ENCFF215TTI ENCFF215TTI.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 4.5 GB link
ENCFF605UTR ENCFF605UTR.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 5.5 GB link
ENCFF792JJE ENCFF792JJE.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 4.6 GB link
ENCFF799ITP ENCFF799ITP.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 5.5 GB link
ENCFF979KKR ENCFF979KKR.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 4.6 GB link
ENCFF555GLH ENCFF555GLH.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V24 transcriptome alignments GRCh38 6.5 GB link
ENCFF880SFD ENCFF880SFD.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V24 transcriptome alignments GRCh38 6.3 GB link
ENCFF509COT ENCFF509COT.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V29 transcriptome alignments GRCh38 7.4 GB link
ENCFF818UJS ENCFF818UJS.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V29 transcriptome alignments GRCh38 7.1 GB link
ENCFF209MHY ENCFF209MHY.bam bam (transcriptome alignments); assembly: hg19; genome annotation: V19 transcriptome alignments hg19 6.2 GB link
ENCFF430THL ENCFF430THL.bam bam (transcriptome alignments); assembly: hg19; genome annotation: V19 transcriptome alignments hg19 6.4 GB link
ENCFF501EZQ ENCFF501EZQ.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 103.5 MB link
ENCFF580NDY ENCFF580NDY.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 86.9 MB link
ENCFF590DNE ENCFF590DNE.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 99.4 MB link
ENCFF747AZZ ENCFF747AZZ.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 90.6 MB link
ENCFF382IDP ENCFF382IDP.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V29 minus strand signal of all reads GRCh38 103.5 MB link
ENCFF917FOP ENCFF917FOP.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V29 minus strand signal of all reads GRCh38 99.4 MB link
ENCFF036KMK ENCFF036KMK.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 102.3 MB link
ENCFF159EYG ENCFF159EYG.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 92.8 MB link
ENCFF197MIJ ENCFF197MIJ.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 88.6 MB link
ENCFF222HFH ENCFF222HFH.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 89.2 MB link
ENCFF481LZH ENCFF481LZH.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 98.1 MB link
ENCFF690WHX ENCFF690WHX.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 84.3 MB link
ENCFF156EER ENCFF156EER.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 80.5 MB link
ENCFF461BBN ENCFF461BBN.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 84.7 MB link
ENCFF541HCJ ENCFF541HCJ.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 91.5 MB link
ENCFF906OJA ENCFF906OJA.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 87.6 MB link
ENCFF178JKO ENCFF178JKO.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 minus strand signal of unique reads GRCh38 90.7 MB link
ENCFF784AIU ENCFF784AIU.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 minus strand signal of unique reads GRCh38 86.7 MB link
ENCFF193PXW ENCFF193PXW.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 87.4 MB link
ENCFF505QPQ ENCFF505QPQ.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 84.1 MB link
ENCFF560OEN ENCFF560OEN.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 81.0 MB link
ENCFF565DPS ENCFF565DPS.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 90.8 MB link
ENCFF655ZTK ENCFF655ZTK.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 77.7 MB link
ENCFF715AXB ENCFF715AXB.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 81.4 MB link
ENCFF189YUV ENCFF189YUV.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 87.9 MB link
ENCFF309SNF ENCFF309SNF.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 91.7 MB link
ENCFF431NPI ENCFF431NPI.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 104.6 MB link
ENCFF900UYE ENCFF900UYE.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 100.4 MB link
ENCFF264QYH ENCFF264QYH.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V29 plus strand signal of all reads GRCh38 104.6 MB link
ENCFF541TWX ENCFF541TWX.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V29 plus strand signal of all reads GRCh38 100.5 MB link
ENCFF134YAC ENCFF134YAC.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 103.5 MB link
ENCFF262IPT ENCFF262IPT.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 99.3 MB link
ENCFF503FNM ENCFF503FNM.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 85.8 MB link
ENCFF552YVN ENCFF552YVN.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 94.3 MB link
ENCFF770NWX ENCFF770NWX.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 90.0 MB link
ENCFF882YFB ENCFF882YFB.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 90.6 MB link
ENCFF411CFG ENCFF411CFG.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 86.5 MB link
ENCFF642PNV ENCFF642PNV.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 82.1 MB link
ENCFF890BPR ENCFF890BPR.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 93.5 MB link
ENCFF995KHV ENCFF995KHV.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 89.6 MB link
ENCFF647CGG ENCFF647CGG.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 plus strand signal of unique reads GRCh38 88.7 MB link
ENCFF957RLT ENCFF957RLT.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 plus strand signal of unique reads GRCh38 92.7 MB link
ENCFF008UMY ENCFF008UMY.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 83.5 MB link
ENCFF010PRA ENCFF010PRA.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 79.8 MB link
ENCFF050PXP ENCFF050PXP.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 86.2 MB link
ENCFF145CVK ENCFF145CVK.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 89.5 MB link
ENCFF150IIL ENCFF150IIL.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 83.0 MB link
ENCFF745XYI ENCFF745XYI.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 93.0 MB link
ENCFF423TCH ENCFF423TCH.fastq fastq (reads) reads 3.0 GB link
ENCFF508RPC ENCFF508RPC.fastq fastq (reads) reads 3.0 GB link
ENCFF836KMN ENCFF836KMN.fastq fastq (reads) reads 3.1 GB link
ENCFF973JAQ ENCFF973JAQ.fastq fastq (reads) reads 2.9 GB link
ENCFF208SEB ENCFF208SEB.tar tar (differential splicing quantifications); assembly: hg19; genome annotation: V19 differential splicing quantifications hg19 5.0 MB link
ENCFF214FLR ENCFF214FLR.tar tar (differential splicing quantifications); assembly: hg19; genome annotation: V19 differential splicing quantifications hg19 16.4 MB link
ENCFF642MAP ENCFF642MAP.tar tar (differential splicing quantifications); assembly: hg19; genome annotation: V19 differential splicing quantifications hg19 4.2 MB link
ENCFF142DIR ENCFF142DIR.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 1.6 MB link
ENCFF596LIF ENCFF596LIF.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 2.0 MB link
ENCFF599IUI ENCFF599IUI.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 2.7 MB link
ENCFF639VBQ ENCFF639VBQ.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 4.4 MB link
ENCFF814SAO ENCFF814SAO.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 5.6 MB link
ENCFF250DCF ENCFF250DCF.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V24 gene quantifications GRCh38 9.5 MB link
ENCFF604ZCA ENCFF604ZCA.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V24 gene quantifications GRCh38 9.5 MB link
ENCFF438LWB ENCFF438LWB.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V29 gene quantifications GRCh38 10.4 MB link
ENCFF559TZM ENCFF559TZM.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V29 gene quantifications GRCh38 10.4 MB link
ENCFF075QNL ENCFF075QNL.tsv tsv (gene quantifications); assembly: hg19; genome annotation: V19 gene quantifications hg19 9.1 MB link
ENCFF416MHI ENCFF416MHI.tsv tsv (gene quantifications); assembly: hg19; genome annotation: V19 gene quantifications hg19 9.1 MB link
ENCFF426GWJ ENCFF426GWJ.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V24 transcript quantifications GRCh38 25.3 MB link
ENCFF928NGM ENCFF928NGM.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V24 transcript quantifications GRCh38 25.3 MB link
ENCFF390TAJ ENCFF390TAJ.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 27.4 MB link
ENCFF594THM ENCFF594THM.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 29.8 MB link
ENCFF657IWC ENCFF657IWC.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 27.4 MB link
ENCFF991IXS ENCFF991IXS.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 29.8 MB link
ENCFF066QND ENCFF066QND.tsv tsv (transcript quantifications); assembly: hg19; genome annotation: V19 transcript quantifications hg19 24.9 MB link
ENCFF941ZTP ENCFF941ZTP.tsv tsv (transcript quantifications); assembly: hg19; genome annotation: V19 transcript quantifications hg19 24.9 MB link