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ENCSR624XHG

ENCSR ENCODE
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RNA-seq on K562 cells treated with an shRNA knockdown against RNASEN. (RNASEN50_BGKLV28)

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

Summary

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

Overall Design

RNA-seq on K562 cells treated with an shRNA knockdown against RNASEN. (RNASEN50_BGKLV28)

Analysis

View Data Processing
Analysis page is available for ENCSR624XHG.

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: 134.1 GB
Assay: shRNA RNA-seq
Target: DROSHA
Biosample: Homo sapiens K562 expressing RNAi targeting H. sapiens DROSHA
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
ENCFF204IXM ENCFF204IXM.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 4.5 GB link
ENCFF245BDJ ENCFF245BDJ.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 5.2 GB link
ENCFF520WPX ENCFF520WPX.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 5.6 GB link
ENCFF944XRF ENCFF944XRF.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 6.5 GB link
ENCFF601TYU ENCFF601TYU.bam bam (alignments); assembly: GRCh38; genome annotation: V29 alignments GRCh38 6.6 GB link
ENCFF634FHW ENCFF634FHW.bam bam (alignments); assembly: GRCh38; genome annotation: V29 alignments GRCh38 5.6 GB link
ENCFF126VJO ENCFF126VJO.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 4.5 GB link
ENCFF362VKF ENCFF362VKF.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 5.6 GB link
ENCFF382SWC ENCFF382SWC.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 6.4 GB link
ENCFF475GCB ENCFF475GCB.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 5.2 GB link
ENCFF772BWX ENCFF772BWX.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 4.5 GB link
ENCFF803YDM ENCFF803YDM.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 5.2 GB link
ENCFF259PPF ENCFF259PPF.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V24 transcriptome alignments GRCh38 7.3 GB link
ENCFF377KCC ENCFF377KCC.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V24 transcriptome alignments GRCh38 8.5 GB link
ENCFF155QSK ENCFF155QSK.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V29 transcriptome alignments GRCh38 9.7 GB link
ENCFF398WDB ENCFF398WDB.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V29 transcriptome alignments GRCh38 8.4 GB link
ENCFF490NYC ENCFF490NYC.bam bam (transcriptome alignments); assembly: hg19; genome annotation: V19 transcriptome alignments hg19 8.4 GB link
ENCFF577SWG ENCFF577SWG.bam bam (transcriptome alignments); assembly: hg19; genome annotation: V19 transcriptome alignments hg19 7.3 GB link
ENCFF306APY ENCFF306APY.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 118.9 MB link
ENCFF826VFR ENCFF826VFR.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 89.5 MB link
ENCFF855XIJ ENCFF855XIJ.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 105.9 MB link
ENCFF989FFV ENCFF989FFV.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 102.1 MB link
ENCFF012PAP ENCFF012PAP.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V29 minus strand signal of all reads GRCh38 118.9 MB link
ENCFF562NVB ENCFF562NVB.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V29 minus strand signal of all reads GRCh38 102.1 MB link
ENCFF114WCP ENCFF114WCP.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 108.3 MB link
ENCFF402EZW ENCFF402EZW.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 88.4 MB link
ENCFF405UDH ENCFF405UDH.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 100.6 MB link
ENCFF607YSC ENCFF607YSC.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 116.8 MB link
ENCFF908GII ENCFF908GII.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 105.2 MB link
ENCFF996DRC ENCFF996DRC.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 91.1 MB link
ENCFF186CXG ENCFF186CXG.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 97.2 MB link
ENCFF404BVC ENCFF404BVC.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 88.4 MB link
ENCFF724MNO ENCFF724MNO.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 102.9 MB link
ENCFF920ZRH ENCFF920ZRH.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 82.6 MB link
ENCFF157QDG ENCFF157QDG.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 minus strand signal of unique reads GRCh38 88.9 MB link
ENCFF618RBA ENCFF618RBA.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 minus strand signal of unique reads GRCh38 103.9 MB link
ENCFF120YLV ENCFF120YLV.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 98.3 MB link
ENCFF161SDP ENCFF161SDP.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 81.2 MB link
ENCFF278QDW ENCFF278QDW.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 82.5 MB link
ENCFF381YYY ENCFF381YYY.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 89.0 MB link
ENCFF739FKP ENCFF739FKP.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 96.0 MB link
ENCFF833ZZN ENCFF833ZZN.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 103.4 MB link
ENCFF142HEJ ENCFF142HEJ.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 119.9 MB link
ENCFF466PBI ENCFF466PBI.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 103.3 MB link
ENCFF622NGU ENCFF622NGU.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 107.0 MB link
ENCFF779SKP ENCFF779SKP.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 90.6 MB link
ENCFF834IMD ENCFF834IMD.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V29 plus strand signal of all reads GRCh38 103.3 MB link
ENCFF897YYC ENCFF897YYC.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V29 plus strand signal of all reads GRCh38 119.9 MB link
ENCFF424KHO ENCFF424KHO.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 102.0 MB link
ENCFF444PQS ENCFF444PQS.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 92.7 MB link
ENCFF697YJW ENCFF697YJW.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 118.1 MB link
ENCFF709WDU ENCFF709WDU.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 90.0 MB link
ENCFF835GLF ENCFF835GLF.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 110.1 MB link
ENCFF943ZKS ENCFF943ZKS.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 106.9 MB link
ENCFF503GSW ENCFF503GSW.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 99.0 MB link
ENCFF615WGE ENCFF615WGE.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 105.0 MB link
ENCFF660EZD ENCFF660EZD.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 90.3 MB link
ENCFF839OEK ENCFF839OEK.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 84.3 MB link
ENCFF131GXH ENCFF131GXH.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 plus strand signal of unique reads GRCh38 90.8 MB link
ENCFF425XBR ENCFF425XBR.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 plus strand signal of unique reads GRCh38 106.0 MB link
ENCFF294ABN ENCFF294ABN.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 100.6 MB link
ENCFF329PPH ENCFF329PPH.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 98.5 MB link
ENCFF356EEX ENCFF356EEX.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 84.5 MB link
ENCFF445AXE ENCFF445AXE.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 91.2 MB link
ENCFF446IDQ ENCFF446IDQ.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 83.4 MB link
ENCFF452OFU ENCFF452OFU.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 105.7 MB link
ENCFF154YPK ENCFF154YPK.fastq fastq (reads) reads 3.8 GB link
ENCFF294QPX ENCFF294QPX.fastq fastq (reads) reads 3.3 GB link
ENCFF378AUD ENCFF378AUD.fastq fastq (reads) reads 3.2 GB link
ENCFF649TZL ENCFF649TZL.fastq fastq (reads) reads 3.7 GB link
ENCFF467VSO ENCFF467VSO.tar tar (differential splicing quantifications); assembly: hg19; genome annotation: V19 differential splicing quantifications hg19 17.0 MB link
ENCFF774EZG ENCFF774EZG.tar tar (differential splicing quantifications); assembly: hg19; genome annotation: V19 differential splicing quantifications hg19 4.1 MB link
ENCFF926NRS ENCFF926NRS.tar tar (differential splicing quantifications); assembly: hg19; genome annotation: V19 differential splicing quantifications hg19 5.1 MB link
ENCFF067JET ENCFF067JET.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 1.9 MB link
ENCFF269VLX ENCFF269VLX.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 2.8 MB link
ENCFF292BWQ ENCFF292BWQ.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 1.6 MB link
ENCFF307TTC ENCFF307TTC.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 4.2 MB link
ENCFF747BCJ ENCFF747BCJ.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 5.7 MB link
ENCFF129DKP ENCFF129DKP.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V24 gene quantifications GRCh38 9.5 MB link
ENCFF427JWG ENCFF427JWG.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V24 gene quantifications GRCh38 9.5 MB link
ENCFF786DIH ENCFF786DIH.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V29 gene quantifications GRCh38 10.4 MB link
ENCFF937LAI ENCFF937LAI.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V29 gene quantifications GRCh38 10.4 MB link
ENCFF104OHS ENCFF104OHS.tsv tsv (gene quantifications); assembly: hg19; genome annotation: V19 gene quantifications hg19 9.1 MB link
ENCFF809TWR ENCFF809TWR.tsv tsv (gene quantifications); assembly: hg19; genome annotation: V19 gene quantifications hg19 9.1 MB link
ENCFF100EKM ENCFF100EKM.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V24 transcript quantifications GRCh38 25.4 MB link
ENCFF921DYM ENCFF921DYM.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V24 transcript quantifications GRCh38 25.4 MB link
ENCFF722WSR ENCFF722WSR.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 27.5 MB link
ENCFF815TSM ENCFF815TSM.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 27.4 MB link
ENCFF869EAM ENCFF869EAM.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 29.9 MB link
ENCFF876HQP ENCFF876HQP.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 29.9 MB link
ENCFF334UMF ENCFF334UMF.tsv tsv (transcript quantifications); assembly: hg19; genome annotation: V19 transcript quantifications hg19 25.0 MB link
ENCFF575EAN ENCFF575EAN.tsv tsv (transcript quantifications); assembly: hg19; genome annotation: V19 transcript quantifications hg19 24.9 MB link