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ENCSR721MXZ

ENCSR ENCODE
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RNA-seq on K562 cells treated with an shRNA knockdown against ABCF1. (ABCF1_BGKLV29)

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

Summary

shRNA RNA-seq of ABCF1 in Homo sapiens K562 expressing RNAi targeting H. sapiens ABCF1

Overall Design

RNA-seq on K562 cells treated with an shRNA knockdown against ABCF1. (ABCF1_BGKLV29)

Analysis

View Data Processing
Analysis page is available for ENCSR721MXZ.

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: 213.3 GB
Assay: shRNA RNA-seq
Target: ABCF1
Biosample: Homo sapiens K562 expressing RNAi targeting H. sapiens ABCF1
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
ENCFF276IWT ENCFF276IWT.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 10.8 GB link
ENCFF349IYQ ENCFF349IYQ.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 8.9 GB link
ENCFF519FBY ENCFF519FBY.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 10.7 GB link
ENCFF903PZV ENCFF903PZV.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 8.8 GB link
ENCFF285LXS ENCFF285LXS.bam bam (alignments); assembly: GRCh38; genome annotation: V29 alignments GRCh38 10.8 GB link
ENCFF410WYF ENCFF410WYF.bam bam (alignments); assembly: GRCh38; genome annotation: V29 alignments GRCh38 10.7 GB link
ENCFF032JJO ENCFF032JJO.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 8.7 GB link
ENCFF092DQF ENCFF092DQF.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 8.8 GB link
ENCFF146LDM ENCFF146LDM.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 8.8 GB link
ENCFF494AFA ENCFF494AFA.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 10.4 GB link
ENCFF642YMU ENCFF642YMU.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 10.5 GB link
ENCFF661IOX ENCFF661IOX.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 8.7 GB link
ENCFF445EFX ENCFF445EFX.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V24 transcriptome alignments GRCh38 11.1 GB link
ENCFF867JYY ENCFF867JYY.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V24 transcriptome alignments GRCh38 11.0 GB link
ENCFF428BTW ENCFF428BTW.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V29 transcriptome alignments GRCh38 12.3 GB link
ENCFF955CWV ENCFF955CWV.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V29 transcriptome alignments GRCh38 12.5 GB link
ENCFF074VRT ENCFF074VRT.bam bam (transcriptome alignments); assembly: hg19; genome annotation: V19 transcriptome alignments hg19 11.0 GB link
ENCFF504WFJ ENCFF504WFJ.bam bam (transcriptome alignments); assembly: hg19; genome annotation: V19 transcriptome alignments hg19 10.9 GB link
ENCFF724XFO ENCFF724XFO.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 108.5 MB link
ENCFF805YLV ENCFF805YLV.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 112.2 MB link
ENCFF965HEL ENCFF965HEL.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 129.1 MB link
ENCFF980KOA ENCFF980KOA.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 133.2 MB link
ENCFF360UPR ENCFF360UPR.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V29 minus strand signal of all reads GRCh38 129.1 MB link
ENCFF466NWI ENCFF466NWI.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V29 minus strand signal of all reads GRCh38 133.2 MB link
ENCFF159UTK ENCFF159UTK.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 130.6 MB link
ENCFF231UTK ENCFF231UTK.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 114.2 MB link
ENCFF315CAL ENCFF315CAL.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 111.5 MB link
ENCFF442ILU ENCFF442ILU.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 109.7 MB link
ENCFF887QJN ENCFF887QJN.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 106.6 MB link
ENCFF897TBN ENCFF897TBN.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 127.8 MB link
ENCFF132ZTG ENCFF132ZTG.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 101.1 MB link
ENCFF349YMM ENCFF349YMM.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 103.6 MB link
ENCFF381AVU ENCFF381AVU.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 113.1 MB link
ENCFF641NCU ENCFF641NCU.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 115.1 MB link
ENCFF900KJE ENCFF900KJE.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 minus strand signal of unique reads GRCh38 115.2 MB link
ENCFF966IAN ENCFF966IAN.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 minus strand signal of unique reads GRCh38 112.3 MB link
ENCFF066YRG ENCFF066YRG.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 96.7 MB link
ENCFF266AZO ENCFF266AZO.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 114.8 MB link
ENCFF353QPW ENCFF353QPW.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 113.3 MB link
ENCFF509DKD ENCFF509DKD.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 105.0 MB link
ENCFF704MFD ENCFF704MFD.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 101.8 MB link
ENCFF886TXY ENCFF886TXY.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 100.3 MB link
ENCFF057DZW ENCFF057DZW.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 134.4 MB link
ENCFF293ZQG ENCFF293ZQG.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 130.2 MB link
ENCFF382VRG ENCFF382VRG.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 109.7 MB link
ENCFF558EDJ ENCFF558EDJ.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 113.5 MB link
ENCFF571DIG ENCFF571DIG.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V29 plus strand signal of all reads GRCh38 134.4 MB link
ENCFF592BYK ENCFF592BYK.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V29 plus strand signal of all reads GRCh38 130.2 MB link
ENCFF064ISZ ENCFF064ISZ.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 111.5 MB link
ENCFF092RDA ENCFF092RDA.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 129.0 MB link
ENCFF245URE ENCFF245URE.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 131.8 MB link
ENCFF345CYE ENCFF345CYE.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 115.9 MB link
ENCFF369KEJ ENCFF369KEJ.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 113.2 MB link
ENCFF774XAD ENCFF774XAD.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 108.3 MB link
ENCFF366XXH ENCFF366XXH.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 105.6 MB link
ENCFF505BNL ENCFF505BNL.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 115.2 MB link
ENCFF702FXB ENCFF702FXB.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 117.2 MB link
ENCFF916PWJ ENCFF916PWJ.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 103.0 MB link
ENCFF803QWQ ENCFF803QWQ.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 plus strand signal of unique reads GRCh38 117.4 MB link
ENCFF831QRG ENCFF831QRG.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 plus strand signal of unique reads GRCh38 114.5 MB link
ENCFF212SSS ENCFF212SSS.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 117.2 MB link
ENCFF241ZYD ENCFF241ZYD.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 104.1 MB link
ENCFF281VIE ENCFF281VIE.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 102.9 MB link
ENCFF384GGO ENCFF384GGO.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 99.2 MB link
ENCFF552TRL ENCFF552TRL.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 107.5 MB link
ENCFF649NQU ENCFF649NQU.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 115.7 MB link
ENCFF082HTI ENCFF082HTI.fastq fastq (reads) reads 5.5 GB link
ENCFF444LJL ENCFF444LJL.fastq fastq (reads) reads 5.6 GB link
ENCFF552MNU ENCFF552MNU.fastq fastq (reads) reads 5.6 GB link
ENCFF719MPH ENCFF719MPH.fastq fastq (reads) reads 5.5 GB link
ENCFF038WLG ENCFF038WLG.tar tar (differential splicing quantifications); assembly: hg19; genome annotation: V19 differential splicing quantifications hg19 16.3 MB link
ENCFF359WLF ENCFF359WLF.tar tar (differential splicing quantifications); assembly: hg19; genome annotation: V19 differential splicing quantifications hg19 5.2 MB link
ENCFF798EIB ENCFF798EIB.tar tar (differential splicing quantifications); assembly: hg19; genome annotation: V19 differential splicing quantifications hg19 4.3 MB link
ENCFF070YWT ENCFF070YWT.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 4.4 MB link
ENCFF365XCH ENCFF365XCH.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 2.0 MB link
ENCFF543AWA ENCFF543AWA.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 2.9 MB link
ENCFF715QGC ENCFF715QGC.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 5.6 MB link
ENCFF885DEK ENCFF885DEK.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 1.7 MB link
ENCFF498KDG ENCFF498KDG.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V24 gene quantifications GRCh38 9.5 MB link
ENCFF662EUV ENCFF662EUV.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V24 gene quantifications GRCh38 9.5 MB link
ENCFF515XIO ENCFF515XIO.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V29 gene quantifications GRCh38 10.4 MB link
ENCFF825OAK ENCFF825OAK.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V29 gene quantifications GRCh38 10.4 MB link
ENCFF123IWZ ENCFF123IWZ.tsv tsv (gene quantifications); assembly: hg19; genome annotation: V19 gene quantifications hg19 9.1 MB link
ENCFF836CNC ENCFF836CNC.tsv tsv (gene quantifications); assembly: hg19; genome annotation: V19 gene quantifications hg19 9.1 MB link
ENCFF184JZF ENCFF184JZF.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V24 transcript quantifications GRCh38 25.4 MB link
ENCFF616XHE ENCFF616XHE.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V24 transcript quantifications GRCh38 25.4 MB link
ENCFF075USA ENCFF075USA.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 29.9 MB link
ENCFF264ZGK ENCFF264ZGK.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 27.5 MB link
ENCFF712TWV ENCFF712TWV.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 29.9 MB link
ENCFF728DBO ENCFF728DBO.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 27.5 MB link
ENCFF142RJC ENCFF142RJC.tsv tsv (transcript quantifications); assembly: hg19; genome annotation: V19 transcript quantifications hg19 25.0 MB link
ENCFF532OAV ENCFF532OAV.tsv tsv (transcript quantifications); assembly: hg19; genome annotation: V19 transcript quantifications hg19 24.9 MB link