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ENCSR618IQH

ENCSR ENCODE
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RNA-seq on K562 cells treated with an shRNA knockdown against PUS1. (PUS1_BGKLV32)

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

Summary

shRNA RNA-seq of PUS1 in Homo sapiens K562 expressing RNAi targeting H. sapiens PUS1

Overall Design

RNA-seq on K562 cells treated with an shRNA knockdown against PUS1. (PUS1_BGKLV32)

Analysis

View Data Processing
Analysis page is available for ENCSR618IQH.

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: 167.2 GB
Assay: shRNA RNA-seq
Target: PUS1
Biosample: Homo sapiens K562 expressing RNAi targeting H. sapiens PUS1
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
ENCFF364LVH ENCFF364LVH.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 10.6 GB link
ENCFF382NFR ENCFF382NFR.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 8.5 GB link
ENCFF769FYD ENCFF769FYD.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 5.4 GB link
ENCFF923DHP ENCFF923DHP.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 6.7 GB link
ENCFF623QKM ENCFF623QKM.bam bam (alignments); assembly: GRCh38; genome annotation: V29 alignments GRCh38 6.7 GB link
ENCFF941DFX ENCFF941DFX.bam bam (alignments); assembly: GRCh38; genome annotation: V29 alignments GRCh38 10.6 GB link
ENCFF160QDQ ENCFF160QDQ.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 7.9 GB link
ENCFF185DVW ENCFF185DVW.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 5.0 GB link
ENCFF722UNY ENCFF722UNY.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 9.6 GB link
ENCFF775UPA ENCFF775UPA.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 6.0 GB link
ENCFF796KSS ENCFF796KSS.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 7.9 GB link
ENCFF902AYT ENCFF902AYT.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 5.0 GB link
ENCFF499LUT ENCFF499LUT.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V24 transcriptome alignments GRCh38 10.8 GB link
ENCFF616BIS ENCFF616BIS.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V24 transcriptome alignments GRCh38 6.5 GB link
ENCFF873JLA ENCFF873JLA.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V29 transcriptome alignments GRCh38 12.2 GB link
ENCFF959YLW ENCFF959YLW.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V29 transcriptome alignments GRCh38 7.4 GB link
ENCFF041MWW ENCFF041MWW.bam bam (transcriptome alignments); assembly: hg19; genome annotation: V19 transcriptome alignments hg19 10.7 GB link
ENCFF803ZMS ENCFF803ZMS.bam bam (transcriptome alignments); assembly: hg19; genome annotation: V19 transcriptome alignments hg19 6.5 GB link
ENCFF098CVZ ENCFF098CVZ.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 138.6 MB link
ENCFF468MNF ENCFF468MNF.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 94.3 MB link
ENCFF711DBY ENCFF711DBY.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 107.9 MB link
ENCFF870PAI ENCFF870PAI.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 121.3 MB link
ENCFF181CYU ENCFF181CYU.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V29 minus strand signal of all reads GRCh38 108.0 MB link
ENCFF402BNO ENCFF402BNO.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V29 minus strand signal of all reads GRCh38 138.6 MB link
ENCFF079CYX ENCFF079CYX.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 107.8 MB link
ENCFF081FRK ENCFF081FRK.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 93.9 MB link
ENCFF350BOO ENCFF350BOO.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 122.6 MB link
ENCFF549TCF ENCFF549TCF.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 96.6 MB link
ENCFF584XZO ENCFF584XZO.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 124.2 MB link
ENCFF634IFB ENCFF634IFB.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 136.6 MB link
ENCFF114GYF ENCFF114GYF.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 114.5 MB link
ENCFF430HRQ ENCFF430HRQ.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 96.9 MB link
ENCFF787OYQ ENCFF787OYQ.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 89.5 MB link
ENCFF952LOB ENCFF952LOB.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 122.7 MB link
ENCFF362QIV ENCFF362QIV.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 minus strand signal of unique reads GRCh38 97.5 MB link
ENCFF755TFN ENCFF755TFN.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 minus strand signal of unique reads GRCh38 123.0 MB link
ENCFF161LDD ENCFF161LDD.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 123.3 MB link
ENCFF334MHB ENCFF334MHB.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 97.3 MB link
ENCFF364WXC ENCFF364WXC.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 112.6 MB link
ENCFF569YWF ENCFF569YWF.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 114.1 MB link
ENCFF622DGS ENCFF622DGS.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 86.5 MB link
ENCFF899WJJ ENCFF899WJJ.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 89.6 MB link
ENCFF652BZV ENCFF652BZV.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 124.2 MB link
ENCFF917EVO ENCFF917EVO.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 96.6 MB link
ENCFF946XUE ENCFF946XUE.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 141.7 MB link
ENCFF969WPR ENCFF969WPR.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 110.3 MB link
ENCFF219GVM ENCFF219GVM.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V29 plus strand signal of all reads GRCh38 110.4 MB link
ENCFF837SUO ENCFF837SUO.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V29 plus strand signal of all reads GRCh38 141.7 MB link
ENCFF117ZDF ENCFF117ZDF.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 127.7 MB link
ENCFF157OSI ENCFF157OSI.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 96.9 MB link
ENCFF319COC ENCFF319COC.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 139.9 MB link
ENCFF339QXL ENCFF339QXL.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 99.3 MB link
ENCFF560POZ ENCFF560POZ.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 110.3 MB link
ENCFF715VMY ENCFF715VMY.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 126.4 MB link
ENCFF312OPM ENCFF312OPM.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 92.2 MB link
ENCFF407BHA ENCFF407BHA.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 99.9 MB link
ENCFF628GPO ENCFF628GPO.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 118.2 MB link
ENCFF933PYZ ENCFF933PYZ.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 126.6 MB link
ENCFF363WYR ENCFF363WYR.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 plus strand signal of unique reads GRCh38 126.9 MB link
ENCFF390YTE ENCFF390YTE.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 plus strand signal of unique reads GRCh38 100.6 MB link
ENCFF391ZJK ENCFF391ZJK.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 118.1 MB link
ENCFF449FHG ENCFF449FHG.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 100.6 MB link
ENCFF725RGD ENCFF725RGD.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 89.8 MB link
ENCFF754SAP ENCFF754SAP.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 117.1 MB link
ENCFF819VWL ENCFF819VWL.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 127.6 MB link
ENCFF874QFZ ENCFF874QFZ.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 92.7 MB link
ENCFF026KAZ ENCFF026KAZ.fastq fastq (reads) reads 5.3 GB link
ENCFF167BIH ENCFF167BIH.fastq fastq (reads) reads 3.3 GB link
ENCFF734JOA ENCFF734JOA.fastq fastq (reads) reads 3.3 GB link
ENCFF831SXK ENCFF831SXK.fastq fastq (reads) reads 5.4 GB link
ENCFF197OBG ENCFF197OBG.tar tar (differential splicing quantifications); assembly: hg19; genome annotation: V19 differential splicing quantifications hg19 16.6 MB link
ENCFF760EQC ENCFF760EQC.tar tar (differential splicing quantifications); assembly: hg19; genome annotation: V19 differential splicing quantifications hg19 4.6 MB link
ENCFF979PQM ENCFF979PQM.tar tar (differential splicing quantifications); assembly: hg19; genome annotation: V19 differential splicing quantifications hg19 6.5 MB link
ENCFF062WYW ENCFF062WYW.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 1.7 MB link
ENCFF387LKP ENCFF387LKP.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 4.5 MB link
ENCFF580KVK ENCFF580KVK.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 3.0 MB link
ENCFF709VES ENCFF709VES.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 5.5 MB link
ENCFF899DIB ENCFF899DIB.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 2.0 MB link
ENCFF531FHO ENCFF531FHO.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V24 gene quantifications GRCh38 9.5 MB link
ENCFF782GIX ENCFF782GIX.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V24 gene quantifications GRCh38 9.5 MB link
ENCFF598ODP ENCFF598ODP.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V29 gene quantifications GRCh38 10.4 MB link
ENCFF618OAY ENCFF618OAY.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V29 gene quantifications GRCh38 10.4 MB link
ENCFF166GXV ENCFF166GXV.tsv tsv (gene quantifications); assembly: hg19; genome annotation: V19 gene quantifications hg19 9.1 MB link
ENCFF741YZE ENCFF741YZE.tsv tsv (gene quantifications); assembly: hg19; genome annotation: V19 gene quantifications hg19 9.1 MB link
ENCFF351IZO ENCFF351IZO.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V24 transcript quantifications GRCh38 25.4 MB link
ENCFF723LDN ENCFF723LDN.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V24 transcript quantifications GRCh38 25.4 MB link
ENCFF576MGG ENCFF576MGG.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 27.4 MB link
ENCFF691SSF ENCFF691SSF.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 29.9 MB link
ENCFF937OSQ ENCFF937OSQ.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 29.9 MB link
ENCFF976OYT ENCFF976OYT.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 27.5 MB link
ENCFF333LLL ENCFF333LLL.tsv tsv (transcript quantifications); assembly: hg19; genome annotation: V19 transcript quantifications hg19 24.9 MB link
ENCFF883ATO ENCFF883ATO.tsv tsv (transcript quantifications); assembly: hg19; genome annotation: V19 transcript quantifications hg19 25.0 MB link