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ENCSR927XBT

ENCSR ENCODE
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RNA-seq on K562 cells treated with an shRNA knockdown against NUSAP1. (NUSAP1_BGKLV21)

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

Summary

shRNA RNA-seq of NUSAP1 in Homo sapiens K562 expressing RNAi targeting H. sapiens NUSAP1

Overall Design

RNA-seq on K562 cells treated with an shRNA knockdown against NUSAP1. (NUSAP1_BGKLV21)

Analysis

View Data Processing
Analysis page is available for ENCSR927XBT.

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: 126.2 GB
Assay: shRNA RNA-seq
Target: NUSAP1
Biosample: Homo sapiens K562 expressing RNAi targeting H. sapiens NUSAP1
Files: 120
Unique ENC file IDs: 120
File Formats
bigWig (63) bam (25) tsv (23) fastq (6) tar (3)
Output types (11)
alignments (17) minus strand signal of all reads (16) minus strand signal of unique reads (16) plus strand signal of all reads (16) plus strand signal of unique reads (15) transcript quantifications (10) gene quantifications (8) transcriptome alignments (8) reads (6) differential expression quantifications (5) differential splicing quantifications (3)

Linked Publications (1)

A large-scale binding and functional map of human RNA-binding proteins.
Nature · 2020

Data Files (120)

Accession File Name Stored Type Output Type Mapping Assembly Size Download
ENCFF407VBF ENCFF407VBF.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 4.4 GB link
ENCFF412VNJ ENCFF412VNJ.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 5.1 GB link
ENCFF453CWB ENCFF453CWB.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 2.9 GB link
ENCFF543SWC ENCFF543SWC.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 6.2 GB link
ENCFF915QCR ENCFF915QCR.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 2.5 GB link
ENCFF948RXH ENCFF948RXH.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 5.4 GB link
ENCFF407XIV ENCFF407XIV.bam bam (alignments); assembly: GRCh38; genome annotation: V29 alignments GRCh38 2.9 GB link
ENCFF519SQN ENCFF519SQN.bam bam (alignments); assembly: GRCh38; genome annotation: V29 alignments GRCh38 5.4 GB link
ENCFF146JAP ENCFF146JAP.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 1.7 GB link
ENCFF204APB ENCFF204APB.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 2.4 GB link
ENCFF437BIF ENCFF437BIF.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 5.2 GB link
ENCFF591KID ENCFF591KID.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 2.9 GB link
ENCFF693ZJX ENCFF693ZJX.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 1.7 GB link
ENCFF724WZZ ENCFF724WZZ.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 5.9 GB link
ENCFF726HWA ENCFF726HWA.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 4.3 GB link
ENCFF745DNT ENCFF745DNT.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 4.9 GB link
ENCFF774TYJ ENCFF774TYJ.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 2.4 GB link
ENCFF682RMG ENCFF682RMG.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V24 transcriptome alignments GRCh38 6.5 GB link
ENCFF776SDA ENCFF776SDA.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V24 transcriptome alignments GRCh38 7.5 GB link
ENCFF873HOR ENCFF873HOR.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V24 transcriptome alignments GRCh38 3.4 GB link
ENCFF419DTB ENCFF419DTB.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V29 transcriptome alignments GRCh38 7.4 GB link
ENCFF852XFS ENCFF852XFS.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V29 transcriptome alignments GRCh38 3.8 GB link
ENCFF156FSY ENCFF156FSY.bam bam (transcriptome alignments); assembly: hg19; genome annotation: V19 transcriptome alignments hg19 7.4 GB link
ENCFF278OYY ENCFF278OYY.bam bam (transcriptome alignments); assembly: hg19; genome annotation: V19 transcriptome alignments hg19 3.3 GB link
ENCFF684NJR ENCFF684NJR.bam bam (transcriptome alignments); assembly: hg19; genome annotation: V19 transcriptome alignments hg19 6.5 GB link
ENCFF074BDW ENCFF074BDW.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 105.6 MB link
ENCFF131MOI ENCFF131MOI.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 62.9 MB link
ENCFF279RBO ENCFF279RBO.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 90.4 MB link
ENCFF651SYW ENCFF651SYW.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 101.4 MB link
ENCFF737TRF ENCFF737TRF.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 56.8 MB link
ENCFF981IZB ENCFF981IZB.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 117.2 MB link
ENCFF049BYT ENCFF049BYT.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V29 minus strand signal of all reads GRCh38 62.9 MB link
ENCFF144LSX ENCFF144LSX.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V29 minus strand signal of all reads GRCh38 101.4 MB link
ENCFF164FTJ ENCFF164FTJ.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 106.7 MB link
ENCFF296LVT ENCFF296LVT.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 53.9 MB link
ENCFF493CTN ENCFF493CTN.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 114.9 MB link
ENCFF621ASW ENCFF621ASW.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 42.5 MB link
ENCFF673ZBS ENCFF673ZBS.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 57.2 MB link
ENCFF756KFH ENCFF756KFH.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 91.7 MB link
ENCFF818FTG ENCFF818FTG.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 62.1 MB link
ENCFF996AYY ENCFF996AYY.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 100.2 MB link
ENCFF256PPO ENCFF256PPO.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 99.7 MB link
ENCFF325ASM ENCFF325ASM.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 84.3 MB link
ENCFF580CGZ ENCFF580CGZ.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 52.6 MB link
ENCFF646BXG ENCFF646BXG.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 105.4 MB link
ENCFF728VLU ENCFF728VLU.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 56.1 MB link
ENCFF878FFE ENCFF878FFE.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 89.6 MB link
ENCFF759IKA ENCFF759IKA.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 minus strand signal of unique reads GRCh38 55.6 MB link
ENCFF805MGK ENCFF805MGK.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 minus strand signal of unique reads GRCh38 89.5 MB link
ENCFF179HQU ENCFF179HQU.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 39.3 MB link
ENCFF295RJX ENCFF295RJX.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 88.6 MB link
ENCFF422YWK ENCFF422YWK.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 84.7 MB link
ENCFF507FYC ENCFF507FYC.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 99.1 MB link
ENCFF510YHI ENCFF510YHI.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 49.7 MB link
ENCFF589NKD ENCFF589NKD.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 55.5 MB link
ENCFF616GRH ENCFF616GRH.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 53.2 MB link
ENCFF718ESB ENCFF718ESB.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 105.3 MB link
ENCFF104BHT ENCFF104BHT.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 57.7 MB link
ENCFF512MJC ENCFF512MJC.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 119.7 MB link
ENCFF556XOF ENCFF556XOF.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 107.9 MB link
ENCFF586RJC ENCFF586RJC.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 102.8 MB link
ENCFF679ZTT ENCFF679ZTT.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 91.6 MB link
ENCFF755BWK ENCFF755BWK.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 63.8 MB link
ENCFF090ZFV ENCFF090ZFV.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V29 plus strand signal of all reads GRCh38 102.7 MB link
ENCFF561EQA ENCFF561EQA.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V29 plus strand signal of all reads GRCh38 63.8 MB link
ENCFF183HVW ENCFF183HVW.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 109.1 MB link
ENCFF412EGL ENCFF412EGL.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 58.2 MB link
ENCFF438DEU ENCFF438DEU.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 43.3 MB link
ENCFF639RJS ENCFF639RJS.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 93.4 MB link
ENCFF668YFC ENCFF668YFC.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 101.5 MB link
ENCFF779QSD ENCFF779QSD.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 117.1 MB link
ENCFF794UTP ENCFF794UTP.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 55.0 MB link
ENCFF837IHJ ENCFF837IHJ.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 63.0 MB link
ENCFF074IJW ENCFF074IJW.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 53.7 MB link
ENCFF075GYV ENCFF075GYV.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 102.6 MB link
ENCFF221VSP ENCFF221VSP.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 108.6 MB link
ENCFF231RCC ENCFF231RCC.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 57.5 MB link
ENCFF428SAS ENCFF428SAS.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 91.6 MB link
ENCFF976NTS ENCFF976NTS.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 86.2 MB link
ENCFF330GCJ ENCFF330GCJ.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 plus strand signal of unique reads GRCh38 91.6 MB link
ENCFF538YVD ENCFF538YVD.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 plus strand signal of unique reads GRCh38 57.0 MB link
ENCFF027ULK ENCFF027ULK.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 102.2 MB link
ENCFF267SFM ENCFF267SFM.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 40.4 MB link
ENCFF685WMS ENCFF685WMS.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 86.9 MB link
ENCFF734QQZ ENCFF734QQZ.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 51.1 MB link
ENCFF792KSR ENCFF792KSR.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 57.0 MB link
ENCFF868BUU ENCFF868BUU.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 90.8 MB link
ENCFF931ALI ENCFF931ALI.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 108.4 MB link
ENCFF071XRK ENCFF071XRK.fastq fastq (reads) reads 1.8 GB link
ENCFF111PUR ENCFF111PUR.fastq fastq (reads) reads 1.6 GB link
ENCFF688AFU ENCFF688AFU.fastq fastq (reads) reads 1.5 GB link
ENCFF712IRZ ENCFF712IRZ.fastq fastq (reads) reads 1.9 GB link
ENCFF903CON ENCFF903CON.fastq fastq (reads) reads 1.1 GB link
ENCFF950FRN ENCFF950FRN.fastq fastq (reads) reads 1.0 GB link
ENCFF190ZDZ ENCFF190ZDZ.tar tar (differential splicing quantifications); assembly: hg19; genome annotation: V19 differential splicing quantifications hg19 4.0 MB link
ENCFF444MXO ENCFF444MXO.tar tar (differential splicing quantifications); assembly: hg19; genome annotation: V19 differential splicing quantifications hg19 3.4 MB link
ENCFF514PQX ENCFF514PQX.tar tar (differential splicing quantifications); assembly: hg19; genome annotation: V19 differential splicing quantifications hg19 14.6 MB link
ENCFF139XOL ENCFF139XOL.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 5.6 MB link
ENCFF605GZC ENCFF605GZC.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 4.2 MB link
ENCFF764XCR ENCFF764XCR.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 2.8 MB link
ENCFF796PHL ENCFF796PHL.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 1.9 MB link
ENCFF852ONK ENCFF852ONK.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 1.8 MB link
ENCFF448TMQ ENCFF448TMQ.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V24 gene quantifications GRCh38 9.5 MB link
ENCFF567PQG ENCFF567PQG.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V24 gene quantifications GRCh38 9.5 MB link
ENCFF621TWV ENCFF621TWV.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V24 gene quantifications GRCh38 9.4 MB link
ENCFF386UKZ ENCFF386UKZ.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V29 gene quantifications GRCh38 10.4 MB link
ENCFF927BCK ENCFF927BCK.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V29 gene quantifications GRCh38 10.4 MB link
ENCFF403XMD ENCFF403XMD.tsv tsv (gene quantifications); assembly: hg19; genome annotation: V19 gene quantifications hg19 9.1 MB link
ENCFF536VHV ENCFF536VHV.tsv tsv (gene quantifications); assembly: hg19; genome annotation: V19 gene quantifications hg19 9.1 MB link
ENCFF682KPH ENCFF682KPH.tsv tsv (gene quantifications); assembly: hg19; genome annotation: V19 gene quantifications hg19 9.1 MB link
ENCFF305SIQ ENCFF305SIQ.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V24 transcript quantifications GRCh38 25.3 MB link
ENCFF489TCD ENCFF489TCD.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V24 transcript quantifications GRCh38 25.4 MB link
ENCFF601IQC ENCFF601IQC.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V24 transcript quantifications GRCh38 25.3 MB link
ENCFF105UZT ENCFF105UZT.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 29.9 MB link
ENCFF164CZI ENCFF164CZI.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 27.2 MB link
ENCFF367DLN ENCFF367DLN.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 27.4 MB link
ENCFF643ZJK ENCFF643ZJK.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 29.8 MB link
ENCFF208OZZ ENCFF208OZZ.tsv tsv (transcript quantifications); assembly: hg19; genome annotation: V19 transcript quantifications hg19 24.9 MB link
ENCFF578HKS ENCFF578HKS.tsv tsv (transcript quantifications); assembly: hg19; genome annotation: V19 transcript quantifications hg19 24.9 MB link
ENCFF579UBA ENCFF579UBA.tsv tsv (transcript quantifications); assembly: hg19; genome annotation: V19 transcript quantifications hg19 24.9 MB link