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ENCSR152IWT

ENCSR ENCODE
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RNA-seq on K562 cells treated with an shRNA knockdown against TRIP6. (TRIP6_BGKLV29)

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

Summary

shRNA RNA-seq of TRIP6 in Homo sapiens K562 expressing RNAi targeting H. sapiens TRIP6

Overall Design

RNA-seq on K562 cells treated with an shRNA knockdown against TRIP6. (TRIP6_BGKLV29)

Analysis

View Data Processing
Analysis page is available for ENCSR152IWT.

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: 123.5 GB
Assay: shRNA RNA-seq
Target: TRIP6
Biosample: Homo sapiens K562 expressing RNAi targeting H. sapiens TRIP6
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
ENCFF172SRF ENCFF172SRF.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 6.9 GB link
ENCFF396OWV ENCFF396OWV.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 3.9 GB link
ENCFF402MEI ENCFF402MEI.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 4.8 GB link
ENCFF899UNY ENCFF899UNY.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 5.6 GB link
ENCFF897ILX ENCFF897ILX.bam bam (alignments); assembly: GRCh38; genome annotation: V29 alignments GRCh38 4.8 GB link
ENCFF903UUL ENCFF903UUL.bam bam (alignments); assembly: GRCh38; genome annotation: V29 alignments GRCh38 6.9 GB link
ENCFF117AJP ENCFF117AJP.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 5.6 GB link
ENCFF195JQS ENCFF195JQS.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 3.9 GB link
ENCFF200LAP ENCFF200LAP.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 6.7 GB link
ENCFF557BIM ENCFF557BIM.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 4.7 GB link
ENCFF767IXP ENCFF767IXP.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 3.9 GB link
ENCFF999GIS ENCFF999GIS.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 5.5 GB link
ENCFF245ZCU ENCFF245ZCU.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V24 transcriptome alignments GRCh38 5.7 GB link
ENCFF592EOU ENCFF592EOU.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V24 transcriptome alignments GRCh38 8.0 GB link
ENCFF017PHK ENCFF017PHK.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V29 transcriptome alignments GRCh38 9.1 GB link
ENCFF240GYQ ENCFF240GYQ.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V29 transcriptome alignments GRCh38 6.5 GB link
ENCFF327JPJ ENCFF327JPJ.bam bam (transcriptome alignments); assembly: hg19; genome annotation: V19 transcriptome alignments hg19 5.6 GB link
ENCFF685JIX ENCFF685JIX.bam bam (transcriptome alignments); assembly: hg19; genome annotation: V19 transcriptome alignments hg19 7.9 GB link
ENCFF273GGP ENCFF273GGP.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 95.1 MB link
ENCFF331XOP ENCFF331XOP.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 102.0 MB link
ENCFF736CQH ENCFF736CQH.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 116.9 MB link
ENCFF849AZH ENCFF849AZH.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 84.6 MB link
ENCFF004KGB ENCFF004KGB.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V29 minus strand signal of all reads GRCh38 95.1 MB link
ENCFF152VEB ENCFF152VEB.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V29 minus strand signal of all reads GRCh38 116.9 MB link
ENCFF231WCG ENCFF231WCG.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 81.6 MB link
ENCFF249QHV ENCFF249QHV.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 94.0 MB link
ENCFF373BZJ ENCFF373BZJ.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 85.6 MB link
ENCFF712KET ENCFF712KET.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 100.9 MB link
ENCFF815OFS ENCFF815OFS.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 105.2 MB link
ENCFF851COV ENCFF851COV.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 114.3 MB link
ENCFF399AAH ENCFF399AAH.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 83.6 MB link
ENCFF618TKY ENCFF618TKY.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 95.2 MB link
ENCFF635LAH ENCFF635LAH.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 78.3 MB link
ENCFF822LNY ENCFF822LNY.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 101.9 MB link
ENCFF092YWL ENCFF092YWL.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 minus strand signal of unique reads GRCh38 101.4 MB link
ENCFF498WMG ENCFF498WMG.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 minus strand signal of unique reads GRCh38 84.0 MB link
ENCFF056SBH ENCFF056SBH.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 78.0 MB link
ENCFF353VAC ENCFF353VAC.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 102.2 MB link
ENCFF447ZCU ENCFF447ZCU.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 83.0 MB link
ENCFF598RBA ENCFF598RBA.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 91.9 MB link
ENCFF736IJC ENCFF736IJC.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 95.4 MB link
ENCFF783DAM ENCFF783DAM.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 75.1 MB link
ENCFF080ECE ENCFF080ECE.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 118.1 MB link
ENCFF258BVA ENCFF258BVA.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 96.0 MB link
ENCFF483BGX ENCFF483BGX.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 103.1 MB link
ENCFF529HVF ENCFF529HVF.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 85.5 MB link
ENCFF502XTB ENCFF502XTB.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V29 plus strand signal of all reads GRCh38 96.0 MB link
ENCFF996PRR ENCFF996PRR.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V29 plus strand signal of all reads GRCh38 118.1 MB link
ENCFF115FQQ ENCFF115FQQ.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 87.0 MB link
ENCFF187ZBP ENCFF187ZBP.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 115.5 MB link
ENCFF467UKG ENCFF467UKG.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 102.6 MB link
ENCFF523CZY ENCFF523CZY.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 106.9 MB link
ENCFF531RTE ENCFF531RTE.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 95.0 MB link
ENCFF691IFY ENCFF691IFY.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 82.9 MB link
ENCFF029JFE ENCFF029JFE.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 85.3 MB link
ENCFF102RFA ENCFF102RFA.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 97.0 MB link
ENCFF609ADO ENCFF609ADO.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 103.9 MB link
ENCFF690QFT ENCFF690QFT.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 79.8 MB link
ENCFF240BUR ENCFF240BUR.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 plus strand signal of unique reads GRCh38 103.4 MB link
ENCFF951ECB ENCFF951ECB.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 plus strand signal of unique reads GRCh38 85.7 MB link
ENCFF239VSX ENCFF239VSX.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 77.0 MB link
ENCFF390NUN ENCFF390NUN.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 104.5 MB link
ENCFF429POD ENCFF429POD.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 97.6 MB link
ENCFF629IFG ENCFF629IFG.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 84.9 MB link
ENCFF859KBA ENCFF859KBA.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 94.3 MB link
ENCFF908DLG ENCFF908DLG.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 79.9 MB link
ENCFF056UJT ENCFF056UJT.fastq fastq (reads) reads 2.6 GB link
ENCFF317XFU ENCFF317XFU.fastq fastq (reads) reads 3.8 GB link
ENCFF360ZPG ENCFF360ZPG.fastq fastq (reads) reads 2.7 GB link
ENCFF601DMJ ENCFF601DMJ.fastq fastq (reads) reads 3.8 GB link
ENCFF340WGL ENCFF340WGL.tar tar (differential splicing quantifications); assembly: hg19; genome annotation: V19 differential splicing quantifications hg19 16.0 MB link
ENCFF419LPB ENCFF419LPB.tar tar (differential splicing quantifications); assembly: hg19; genome annotation: V19 differential splicing quantifications hg19 3.9 MB link
ENCFF633ELM ENCFF633ELM.tar tar (differential splicing quantifications); assembly: hg19; genome annotation: V19 differential splicing quantifications hg19 4.8 MB link
ENCFF163FPA ENCFF163FPA.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 2.9 MB link
ENCFF341SZL ENCFF341SZL.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 5.6 MB link
ENCFF494SWO ENCFF494SWO.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 1.9 MB link
ENCFF817DMB ENCFF817DMB.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 1.8 MB link
ENCFF973YGL ENCFF973YGL.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 4.4 MB link
ENCFF228QIE ENCFF228QIE.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V24 gene quantifications GRCh38 9.5 MB link
ENCFF769ELM ENCFF769ELM.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V24 gene quantifications GRCh38 9.5 MB link
ENCFF178FVA ENCFF178FVA.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V29 gene quantifications GRCh38 10.4 MB link
ENCFF484JEZ ENCFF484JEZ.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V29 gene quantifications GRCh38 10.4 MB link
ENCFF602XVC ENCFF602XVC.tsv tsv (gene quantifications); assembly: hg19; genome annotation: V19 gene quantifications hg19 9.1 MB link
ENCFF631AZW ENCFF631AZW.tsv tsv (gene quantifications); assembly: hg19; genome annotation: V19 gene quantifications hg19 9.1 MB link
ENCFF503PCE ENCFF503PCE.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V24 transcript quantifications GRCh38 25.4 MB link
ENCFF693IQU ENCFF693IQU.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V24 transcript quantifications GRCh38 25.3 MB link
ENCFF071AID ENCFF071AID.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 29.8 MB link
ENCFF163DCS ENCFF163DCS.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 27.5 MB link
ENCFF213AQC ENCFF213AQC.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 27.3 MB link
ENCFF278ZCF ENCFF278ZCF.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 29.9 MB link
ENCFF105JIW ENCFF105JIW.tsv tsv (transcript quantifications); assembly: hg19; genome annotation: V19 transcript quantifications hg19 24.9 MB link
ENCFF524UDY ENCFF524UDY.tsv tsv (transcript quantifications); assembly: hg19; genome annotation: V19 transcript quantifications hg19 24.9 MB link