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ENCSR346DZQ

ENCSR ENCODE
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RNA-seq on K562 cells treated with an shRNA knockdown against NPM1. (NPM1_BGKLV28)

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

Summary

shRNA RNA-seq of NPM1 in Homo sapiens K562 expressing RNAi targeting H. sapiens NPM1

Overall Design

RNA-seq on K562 cells treated with an shRNA knockdown against NPM1. (NPM1_BGKLV28)

Analysis

View Data Processing
Analysis page is available for ENCSR346DZQ.

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: 124.8 GB
Assay: shRNA RNA-seq
Target: NPM1
Biosample: Homo sapiens K562 expressing RNAi targeting H. sapiens NPM1
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
ENCFF547BNZ ENCFF547BNZ.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 4.7 GB link
ENCFF600JAO ENCFF600JAO.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 6.1 GB link
ENCFF629AWY ENCFF629AWY.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 5.7 GB link
ENCFF674FMM ENCFF674FMM.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 4.9 GB link
ENCFF128CTG ENCFF128CTG.bam bam (alignments); assembly: GRCh38; genome annotation: V29 alignments GRCh38 5.7 GB link
ENCFF363FHH ENCFF363FHH.bam bam (alignments); assembly: GRCh38; genome annotation: V29 alignments GRCh38 6.1 GB link
ENCFF107TLV ENCFF107TLV.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 4.6 GB link
ENCFF201SAL ENCFF201SAL.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 4.9 GB link
ENCFF318HDI ENCFF318HDI.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 4.9 GB link
ENCFF625PRU ENCFF625PRU.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 4.6 GB link
ENCFF838WJE ENCFF838WJE.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 5.9 GB link
ENCFF986JGI ENCFF986JGI.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 5.6 GB link
ENCFF248OGO ENCFF248OGO.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V24 transcriptome alignments GRCh38 7.0 GB link
ENCFF370RTV ENCFF370RTV.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V24 transcriptome alignments GRCh38 6.9 GB link
ENCFF188KYP ENCFF188KYP.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V29 transcriptome alignments GRCh38 7.8 GB link
ENCFF243SHP ENCFF243SHP.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V29 transcriptome alignments GRCh38 7.9 GB link
ENCFF098NKK ENCFF098NKK.bam bam (transcriptome alignments); assembly: hg19; genome annotation: V19 transcriptome alignments hg19 6.8 GB link
ENCFF870INK ENCFF870INK.bam bam (transcriptome alignments); assembly: hg19; genome annotation: V19 transcriptome alignments hg19 6.9 GB link
ENCFF257DVK ENCFF257DVK.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 94.6 MB link
ENCFF506KRW ENCFF506KRW.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 86.9 MB link
ENCFF890IOU ENCFF890IOU.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 105.9 MB link
ENCFF907ZYC ENCFF907ZYC.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 101.9 MB link
ENCFF570HDW ENCFF570HDW.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V29 minus strand signal of all reads GRCh38 105.9 MB link
ENCFF970QFS ENCFF970QFS.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V29 minus strand signal of all reads GRCh38 101.9 MB link
ENCFF043XSE ENCFF043XSE.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 99.5 MB link
ENCFF133TRS ENCFF133TRS.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 88.6 MB link
ENCFF281NLI ENCFF281NLI.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 85.2 MB link
ENCFF284PZN ENCFF284PZN.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 95.9 MB link
ENCFF493AWM ENCFF493AWM.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 92.0 MB link
ENCFF541MPX ENCFF541MPX.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 105.7 MB link
ENCFF211XEE ENCFF211XEE.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 87.8 MB link
ENCFF250ZOU ENCFF250ZOU.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 88.8 MB link
ENCFF385TPW ENCFF385TPW.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 94.3 MB link
ENCFF535KPV ENCFF535KPV.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 81.2 MB link
ENCFF116YVJ ENCFF116YVJ.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 minus strand signal of unique reads GRCh38 93.4 MB link
ENCFF945WPD ENCFF945WPD.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 minus strand signal of unique reads GRCh38 89.2 MB link
ENCFF051LFP ENCFF051LFP.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 77.9 MB link
ENCFF217OYM ENCFF217OYM.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 89.0 MB link
ENCFF261EGT ENCFF261EGT.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 93.5 MB link
ENCFF421LMB ENCFF421LMB.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 82.0 MB link
ENCFF427LXV ENCFF427LXV.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 87.9 MB link
ENCFF916EIK ENCFF916EIK.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 81.8 MB link
ENCFF393WNJ ENCFF393WNJ.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 103.4 MB link
ENCFF695BJB ENCFF695BJB.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 107.4 MB link
ENCFF726LPZ ENCFF726LPZ.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 96.0 MB link
ENCFF881AOO ENCFF881AOO.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 88.3 MB link
ENCFF105TTM ENCFF105TTM.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V29 plus strand signal of all reads GRCh38 103.4 MB link
ENCFF578YSM ENCFF578YSM.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V29 plus strand signal of all reads GRCh38 107.4 MB link
ENCFF031QKP ENCFF031QKP.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 90.4 MB link
ENCFF320AAI ENCFF320AAI.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 87.0 MB link
ENCFF489YSB ENCFF489YSB.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 101.0 MB link
ENCFF570CWG ENCFF570CWG.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 93.9 MB link
ENCFF962JXR ENCFF962JXR.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 107.3 MB link
ENCFF993CPG ENCFF993CPG.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 97.8 MB link
ENCFF026NQE ENCFF026NQE.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 96.7 MB link
ENCFF355TWV ENCFF355TWV.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 91.0 MB link
ENCFF552KVY ENCFF552KVY.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 89.8 MB link
ENCFF561ONI ENCFF561ONI.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 83.1 MB link
ENCFF165BFX ENCFF165BFX.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 plus strand signal of unique reads GRCh38 95.8 MB link
ENCFF889SZD ENCFF889SZD.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 plus strand signal of unique reads GRCh38 91.4 MB link
ENCFF412IZR ENCFF412IZR.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 91.4 MB link
ENCFF517SWN ENCFF517SWN.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 84.5 MB link
ENCFF551ZUS ENCFF551ZUS.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 90.4 MB link
ENCFF654DUZ ENCFF654DUZ.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 96.0 MB link
ENCFF900SWS ENCFF900SWS.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 80.1 MB link
ENCFF976UCJ ENCFF976UCJ.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 84.1 MB link
ENCFF261ZCZ ENCFF261ZCZ.fastq fastq (reads) reads 3.2 GB link
ENCFF410BUA ENCFF410BUA.fastq fastq (reads) reads 3.4 GB link
ENCFF569SVK ENCFF569SVK.fastq fastq (reads) reads 3.4 GB link
ENCFF574DCO ENCFF574DCO.fastq fastq (reads) reads 3.2 GB link
ENCFF484MHB ENCFF484MHB.tar tar (differential splicing quantifications); assembly: hg19; genome annotation: V19 differential splicing quantifications hg19 3.7 MB link
ENCFF749HSI ENCFF749HSI.tar tar (differential splicing quantifications); assembly: hg19; genome annotation: V19 differential splicing quantifications hg19 16.5 MB link
ENCFF872GLW ENCFF872GLW.tar tar (differential splicing quantifications); assembly: hg19; genome annotation: V19 differential splicing quantifications hg19 4.6 MB link
ENCFF172YUQ ENCFF172YUQ.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 2.0 MB link
ENCFF385NZR ENCFF385NZR.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 2.7 MB link
ENCFF533LXA ENCFF533LXA.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 4.2 MB link
ENCFF578CKT ENCFF578CKT.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 1.8 MB link
ENCFF712XPP ENCFF712XPP.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 5.5 MB link
ENCFF195MUT ENCFF195MUT.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V24 gene quantifications GRCh38 9.5 MB link
ENCFF910LJY ENCFF910LJY.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V24 gene quantifications GRCh38 9.5 MB link
ENCFF274RPH ENCFF274RPH.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V29 gene quantifications GRCh38 10.4 MB link
ENCFF734IDK ENCFF734IDK.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V29 gene quantifications GRCh38 10.4 MB link
ENCFF056ECX ENCFF056ECX.tsv tsv (gene quantifications); assembly: hg19; genome annotation: V19 gene quantifications hg19 9.1 MB link
ENCFF454XHB ENCFF454XHB.tsv tsv (gene quantifications); assembly: hg19; genome annotation: V19 gene quantifications hg19 9.1 MB link
ENCFF050EEL ENCFF050EEL.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V24 transcript quantifications GRCh38 25.4 MB link
ENCFF166TYP ENCFF166TYP.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V24 transcript quantifications GRCh38 25.4 MB link
ENCFF318JOY ENCFF318JOY.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 29.9 MB link
ENCFF652SPG ENCFF652SPG.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 27.4 MB link
ENCFF744LYB ENCFF744LYB.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 27.4 MB link
ENCFF845BTN ENCFF845BTN.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 29.9 MB link
ENCFF365MWG ENCFF365MWG.tsv tsv (transcript quantifications); assembly: hg19; genome annotation: V19 transcript quantifications hg19 25.0 MB link
ENCFF702VHJ ENCFF702VHJ.tsv tsv (transcript quantifications); assembly: hg19; genome annotation: V19 transcript quantifications hg19 24.9 MB link