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ENCSR034VBA

ENCSR ENCODE
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RNA-seq on K562 cells treated with an shRNA knockdown against HNRNPUL1. (HNRNPUL1_BGKLV28)

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

Summary

shRNA RNA-seq of HNRNPUL1 in Homo sapiens K562 expressing RNAi targeting H. sapiens HNRNPUL1

Overall Design

RNA-seq on K562 cells treated with an shRNA knockdown against HNRNPUL1. (HNRNPUL1_BGKLV28)

Analysis

View Data Processing
Analysis page is available for ENCSR034VBA.

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: 152.1 GB
Assay: shRNA RNA-seq
Target: HNRNPUL1
Biosample: Homo sapiens K562 expressing RNAi targeting H. sapiens HNRNPUL1
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
ENCFF703WDK ENCFF703WDK.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 8.2 GB link
ENCFF769YLX ENCFF769YLX.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 6.7 GB link
ENCFF795GIJ ENCFF795GIJ.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 6.7 GB link
ENCFF914UBT ENCFF914UBT.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 5.5 GB link
ENCFF567GPS ENCFF567GPS.bam bam (alignments); assembly: GRCh38; genome annotation: V29 alignments GRCh38 8.2 GB link
ENCFF578IEY ENCFF578IEY.bam bam (alignments); assembly: GRCh38; genome annotation: V29 alignments GRCh38 6.7 GB link
ENCFF023XBO ENCFF023XBO.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 5.3 GB link
ENCFF032BIU ENCFF032BIU.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 8.0 GB link
ENCFF503VKN ENCFF503VKN.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 6.6 GB link
ENCFF552SMO ENCFF552SMO.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 6.6 GB link
ENCFF650THJ ENCFF650THJ.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 6.4 GB link
ENCFF836HER ENCFF836HER.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 5.4 GB link
ENCFF863HSY ENCFF863HSY.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V24 transcriptome alignments GRCh38 7.2 GB link
ENCFF913OYW ENCFF913OYW.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V24 transcriptome alignments GRCh38 9.3 GB link
ENCFF672KBE ENCFF672KBE.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V29 transcriptome alignments GRCh38 8.1 GB link
ENCFF975WMM ENCFF975WMM.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V29 transcriptome alignments GRCh38 10.5 GB link
ENCFF432KJL ENCFF432KJL.bam bam (transcriptome alignments); assembly: hg19; genome annotation: V19 transcriptome alignments hg19 7.1 GB link
ENCFF686UJA ENCFF686UJA.bam bam (transcriptome alignments); assembly: hg19; genome annotation: V19 transcriptome alignments hg19 9.2 GB link
ENCFF213MVT ENCFF213MVT.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 99.7 MB link
ENCFF481HXS ENCFF481HXS.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 95.4 MB link
ENCFF709PEN ENCFF709PEN.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 109.7 MB link
ENCFF918EQC ENCFF918EQC.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 86.6 MB link
ENCFF656VDI ENCFF656VDI.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V29 minus strand signal of all reads GRCh38 99.7 MB link
ENCFF953KEN ENCFF953KEN.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V29 minus strand signal of all reads GRCh38 109.9 MB link
ENCFF376VHH ENCFF376VHH.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 88.5 MB link
ENCFF435XYN ENCFF435XYN.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 108.1 MB link
ENCFF498JTM ENCFF498JTM.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 98.4 MB link
ENCFF583HSP ENCFF583HSP.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 84.0 MB link
ENCFF648ZHT ENCFF648ZHT.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 93.9 MB link
ENCFF970CPX ENCFF970CPX.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 97.6 MB link
ENCFF162OJP ENCFF162OJP.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 80.4 MB link
ENCFF356HMS ENCFF356HMS.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 95.5 MB link
ENCFF471BHK ENCFF471BHK.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 88.0 MB link
ENCFF699ZOY ENCFF699ZOY.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 87.0 MB link
ENCFF104YWI ENCFF104YWI.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 minus strand signal of unique reads GRCh38 91.3 MB link
ENCFF585EEM ENCFF585EEM.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 minus strand signal of unique reads GRCh38 87.8 MB link
ENCFF008CJJ ENCFF008CJJ.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 86.1 MB link
ENCFF008URU ENCFF008URU.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 95.6 MB link
ENCFF179KDE ENCFF179KDE.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 87.1 MB link
ENCFF452XLX ENCFF452XLX.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 81.0 MB link
ENCFF513BLV ENCFF513BLV.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 89.2 MB link
ENCFF572WXF ENCFF572WXF.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 77.1 MB link
ENCFF334EZM ENCFF334EZM.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 100.9 MB link
ENCFF589UMH ENCFF589UMH.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 96.9 MB link
ENCFF647AQZ ENCFF647AQZ.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 111.2 MB link
ENCFF732TBH ENCFF732TBH.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 87.9 MB link
ENCFF038VJB ENCFF038VJB.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V29 plus strand signal of all reads GRCh38 100.9 MB link
ENCFF276YQD ENCFF276YQD.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V29 plus strand signal of all reads GRCh38 111.4 MB link
ENCFF009MKZ ENCFF009MKZ.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 90.2 MB link
ENCFF132FRD ENCFF132FRD.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 109.7 MB link
ENCFF541MOF ENCFF541MOF.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 85.8 MB link
ENCFF744NSN ENCFF744NSN.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 99.8 MB link
ENCFF752NWG ENCFF752NWG.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 95.8 MB link
ENCFF875LLA ENCFF875LLA.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 99.5 MB link
ENCFF510IKE ENCFF510IKE.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 89.0 MB link
ENCFF564DJH ENCFF564DJH.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 82.2 MB link
ENCFF702ZFG ENCFF702ZFG.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 97.9 MB link
ENCFF982LNH ENCFF982LNH.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 90.1 MB link
ENCFF078GFW ENCFF078GFW.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 plus strand signal of unique reads GRCh38 93.5 MB link
ENCFF469OQX ENCFF469OQX.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 plus strand signal of unique reads GRCh38 89.9 MB link
ENCFF086WFO ENCFF086WFO.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 91.7 MB link
ENCFF241OZK ENCFF241OZK.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 83.1 MB link
ENCFF274OSZ ENCFF274OSZ.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 98.2 MB link
ENCFF418KBT ENCFF418KBT.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 79.3 MB link
ENCFF595MOA ENCFF595MOA.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 88.6 MB link
ENCFF917GOI ENCFF917GOI.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 89.4 MB link
ENCFF312FGA ENCFF312FGA.fastq fastq (reads) reads 3.5 GB link
ENCFF771FXY ENCFF771FXY.fastq fastq (reads) reads 3.5 GB link
ENCFF790GXP ENCFF790GXP.fastq fastq (reads) reads 4.4 GB link
ENCFF903WQO ENCFF903WQO.fastq fastq (reads) reads 4.4 GB link
ENCFF225SXO ENCFF225SXO.tar tar (differential splicing quantifications); assembly: hg19; genome annotation: V19 differential splicing quantifications hg19 5.1 MB link
ENCFF519TEU ENCFF519TEU.tar tar (differential splicing quantifications); assembly: hg19; genome annotation: V19 differential splicing quantifications hg19 4.1 MB link
ENCFF880KVC ENCFF880KVC.tar tar (differential splicing quantifications); assembly: hg19; genome annotation: V19 differential splicing quantifications hg19 16.6 MB link
ENCFF078PZF ENCFF078PZF.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 2.7 MB link
ENCFF138FZZ ENCFF138FZZ.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 4.2 MB link
ENCFF305RCL ENCFF305RCL.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 2.0 MB link
ENCFF884SIG ENCFF884SIG.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 1.6 MB link
ENCFF928RAM ENCFF928RAM.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 5.7 MB link
ENCFF307VSF ENCFF307VSF.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V24 gene quantifications GRCh38 9.5 MB link
ENCFF434BTL ENCFF434BTL.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V24 gene quantifications GRCh38 9.5 MB link
ENCFF375CTE ENCFF375CTE.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V29 gene quantifications GRCh38 10.4 MB link
ENCFF594HYP ENCFF594HYP.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V29 gene quantifications GRCh38 10.4 MB link
ENCFF295WGJ ENCFF295WGJ.tsv tsv (gene quantifications); assembly: hg19; genome annotation: V19 gene quantifications hg19 9.1 MB link
ENCFF993RYQ ENCFF993RYQ.tsv tsv (gene quantifications); assembly: hg19; genome annotation: V19 gene quantifications hg19 9.1 MB link
ENCFF474ERJ ENCFF474ERJ.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V24 transcript quantifications GRCh38 25.4 MB link
ENCFF720UUU ENCFF720UUU.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V24 transcript quantifications GRCh38 25.4 MB link
ENCFF054MZG ENCFF054MZG.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 27.5 MB link
ENCFF165WHQ ENCFF165WHQ.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 29.9 MB link
ENCFF229SNV ENCFF229SNV.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 27.4 MB link
ENCFF650KOW ENCFF650KOW.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 29.9 MB link
ENCFF063NFO ENCFF063NFO.tsv tsv (transcript quantifications); assembly: hg19; genome annotation: V19 transcript quantifications hg19 25.0 MB link
ENCFF787GDJ ENCFF787GDJ.tsv tsv (transcript quantifications); assembly: hg19; genome annotation: V19 transcript quantifications hg19 24.9 MB link