← All datasets

ENCSR770LYW

ENCSR ENCODE
Export SRA CSV View on ENCODE

RNA-seq on K562 cells treated with an shRNA knockdown against SAFB2. (SAFB2_BGKLV24)

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

Summary

shRNA RNA-seq of SAFB2 in Homo sapiens K562 expressing RNAi targeting H. sapiens SAFB2

Overall Design

RNA-seq on K562 cells treated with an shRNA knockdown against SAFB2. (SAFB2_BGKLV24)

Analysis

View Data Processing
Analysis page is available for ENCSR770LYW.

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: 149.3 GB
Assay: shRNA RNA-seq
Target: SAFB2
Biosample: Homo sapiens K562 expressing RNAi targeting H. sapiens SAFB2
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
ENCFF412KKQ ENCFF412KKQ.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 8.6 GB link
ENCFF549ZVX ENCFF549ZVX.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 6.8 GB link
ENCFF879OSQ ENCFF879OSQ.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 7.0 GB link
ENCFF990YUW ENCFF990YUW.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 5.5 GB link
ENCFF221IZS ENCFF221IZS.bam bam (alignments); assembly: GRCh38; genome annotation: V29 alignments GRCh38 6.8 GB link
ENCFF976ZDH ENCFF976ZDH.bam bam (alignments); assembly: GRCh38; genome annotation: V29 alignments GRCh38 8.6 GB link
ENCFF015CAG ENCFF015CAG.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 5.5 GB link
ENCFF198QMX ENCFF198QMX.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 8.4 GB link
ENCFF336WPP ENCFF336WPP.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 5.5 GB link
ENCFF453FCY ENCFF453FCY.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 6.9 GB link
ENCFF605NAW ENCFF605NAW.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 6.6 GB link
ENCFF622TDG ENCFF622TDG.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 6.9 GB link
ENCFF128BQC ENCFF128BQC.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V24 transcriptome alignments GRCh38 8.1 GB link
ENCFF762OPN ENCFF762OPN.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V24 transcriptome alignments GRCh38 6.7 GB link
ENCFF032YKR ENCFF032YKR.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V29 transcriptome alignments GRCh38 9.1 GB link
ENCFF923UZB ENCFF923UZB.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V29 transcriptome alignments GRCh38 7.5 GB link
ENCFF076SVT ENCFF076SVT.bam bam (transcriptome alignments); assembly: hg19; genome annotation: V19 transcriptome alignments hg19 6.6 GB link
ENCFF900GJQ ENCFF900GJQ.bam bam (transcriptome alignments); assembly: hg19; genome annotation: V19 transcriptome alignments hg19 8.1 GB link
ENCFF428DME ENCFF428DME.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 123.1 MB link
ENCFF579FXC ENCFF579FXC.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 79.4 MB link
ENCFF626SEN ENCFF626SEN.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 97.6 MB link
ENCFF915VZV ENCFF915VZV.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 97.4 MB link
ENCFF284VLY ENCFF284VLY.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V29 minus strand signal of all reads GRCh38 97.6 MB link
ENCFF699CWM ENCFF699CWM.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V29 minus strand signal of all reads GRCh38 123.1 MB link
ENCFF270XLH ENCFF270XLH.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 80.7 MB link
ENCFF490MRY ENCFF490MRY.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 121.2 MB link
ENCFF611YNS ENCFF611YNS.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 100.2 MB link
ENCFF619SWX ENCFF619SWX.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 77.3 MB link
ENCFF946UEL ENCFF946UEL.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 94.9 MB link
ENCFF976ROI ENCFF976ROI.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 97.5 MB link
ENCFF094TKE ENCFF094TKE.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 72.7 MB link
ENCFF448DMQ ENCFF448DMQ.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 106.6 MB link
ENCFF647YGX ENCFF647YGX.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 86.3 MB link
ENCFF722IUA ENCFF722IUA.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 90.9 MB link
ENCFF253EPL ENCFF253EPL.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 minus strand signal of unique reads GRCh38 107.1 MB link
ENCFF369TVJ ENCFF369TVJ.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 minus strand signal of unique reads GRCh38 85.5 MB link
ENCFF282QSO ENCFF282QSO.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 106.1 MB link
ENCFF537UFE ENCFF537UFE.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 70.2 MB link
ENCFF569KDS ENCFF569KDS.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 87.0 MB link
ENCFF654VFM ENCFF654VFM.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 85.2 MB link
ENCFF738JAC ENCFF738JAC.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 90.3 MB link
ENCFF961QIX ENCFF961QIX.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 73.6 MB link
ENCFF118GOQ ENCFF118GOQ.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 124.4 MB link
ENCFF226PQD ENCFF226PQD.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 98.4 MB link
ENCFF572EMV ENCFF572EMV.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 98.7 MB link
ENCFF982EXQ ENCFF982EXQ.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 80.3 MB link
ENCFF309GFQ ENCFF309GFQ.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V29 plus strand signal of all reads GRCh38 98.4 MB link
ENCFF354IVN ENCFF354IVN.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V29 plus strand signal of all reads GRCh38 124.4 MB link
ENCFF021EWZ ENCFF021EWZ.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 96.6 MB link
ENCFF162GDZ ENCFF162GDZ.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 81.9 MB link
ENCFF212DEG ENCFF212DEG.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 102.0 MB link
ENCFF287JYN ENCFF287JYN.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 122.6 MB link
ENCFF320LWG ENCFF320LWG.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 78.5 MB link
ENCFF567FLD ENCFF567FLD.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 98.3 MB link
ENCFF074SNE ENCFF074SNE.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 109.0 MB link
ENCFF094WFZ ENCFF094WFZ.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 93.0 MB link
ENCFF478KTK ENCFF478KTK.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 74.2 MB link
ENCFF830SWK ENCFF830SWK.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 87.9 MB link
ENCFF252OGO ENCFF252OGO.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 plus strand signal of unique reads GRCh38 109.5 MB link
ENCFF965QVM ENCFF965QVM.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 plus strand signal of unique reads GRCh38 87.1 MB link
ENCFF011GQA ENCFF011GQA.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 75.4 MB link
ENCFF094PEF ENCFF094PEF.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 87.0 MB link
ENCFF199LDF ENCFF199LDF.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 92.7 MB link
ENCFF376NRL ENCFF376NRL.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 108.7 MB link
ENCFF508SGZ ENCFF508SGZ.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 72.1 MB link
ENCFF699SAK ENCFF699SAK.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 89.4 MB link
ENCFF118BKZ ENCFF118BKZ.fastq fastq (reads) reads 3.4 GB link
ENCFF334WQQ ENCFF334WQQ.fastq fastq (reads) reads 3.5 GB link
ENCFF665ONM ENCFF665ONM.fastq fastq (reads) reads 4.3 GB link
ENCFF707EJL ENCFF707EJL.fastq fastq (reads) reads 4.4 GB link
ENCFF224VYG ENCFF224VYG.tar tar (differential splicing quantifications); assembly: hg19; genome annotation: V19 differential splicing quantifications hg19 16.3 MB link
ENCFF614ESP ENCFF614ESP.tar tar (differential splicing quantifications); assembly: hg19; genome annotation: V19 differential splicing quantifications hg19 4.4 MB link
ENCFF639INV ENCFF639INV.tar tar (differential splicing quantifications); assembly: hg19; genome annotation: V19 differential splicing quantifications hg19 3.9 MB link
ENCFF168SMN ENCFF168SMN.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 4.2 MB link
ENCFF390CDK ENCFF390CDK.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 5.5 MB link
ENCFF754QIP ENCFF754QIP.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 2.9 MB link
ENCFF767GDW ENCFF767GDW.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 2.0 MB link
ENCFF927BNI ENCFF927BNI.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 1.8 MB link
ENCFF673FFS ENCFF673FFS.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V24 gene quantifications GRCh38 9.5 MB link
ENCFF945YKP ENCFF945YKP.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V24 gene quantifications GRCh38 9.5 MB link
ENCFF509WYD ENCFF509WYD.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V29 gene quantifications GRCh38 10.4 MB link
ENCFF582OKB ENCFF582OKB.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V29 gene quantifications GRCh38 10.4 MB link
ENCFF098EJT ENCFF098EJT.tsv tsv (gene quantifications); assembly: hg19; genome annotation: V19 gene quantifications hg19 9.1 MB link
ENCFF194ONM ENCFF194ONM.tsv tsv (gene quantifications); assembly: hg19; genome annotation: V19 gene quantifications hg19 9.1 MB link
ENCFF368VEV ENCFF368VEV.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V24 transcript quantifications GRCh38 25.3 MB link
ENCFF877DPS ENCFF877DPS.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V24 transcript quantifications GRCh38 25.4 MB link
ENCFF148MUB ENCFF148MUB.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 27.4 MB link
ENCFF384MBC ENCFF384MBC.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 29.9 MB link
ENCFF454KIH ENCFF454KIH.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 29.8 MB link
ENCFF644HJG ENCFF644HJG.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 27.5 MB link
ENCFF865JIQ ENCFF865JIQ.tsv tsv (transcript quantifications); assembly: hg19; genome annotation: V19 transcript quantifications hg19 24.9 MB link
ENCFF980XVL ENCFF980XVL.tsv tsv (transcript quantifications); assembly: hg19; genome annotation: V19 transcript quantifications hg19 24.9 MB link