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ENCSR269HQA

ENCSR ENCODE
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RNA-seq on K562 cells treated with an shRNA knockdown against ILF3. (ILF3_BGKLV24)

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

Summary

shRNA RNA-seq of ILF3 in Homo sapiens K562 expressing RNAi targeting H. sapiens ILF3

Overall Design

RNA-seq on K562 cells treated with an shRNA knockdown against ILF3. (ILF3_BGKLV24)

Analysis

View Data Processing
Analysis page is available for ENCSR269HQA.

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: 63.0 GB
Assay: shRNA RNA-seq
Target: ILF3
Biosample: Homo sapiens K562 expressing RNAi targeting H. sapiens ILF3
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
ENCFF067WKG ENCFF067WKG.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 3.1 GB link
ENCFF285BET ENCFF285BET.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 2.7 GB link
ENCFF629QVH ENCFF629QVH.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 2.6 GB link
ENCFF660NLX ENCFF660NLX.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 2.3 GB link
ENCFF236YYQ ENCFF236YYQ.bam bam (alignments); assembly: GRCh38; genome annotation: V29 alignments GRCh38 2.7 GB link
ENCFF705EKL ENCFF705EKL.bam bam (alignments); assembly: GRCh38; genome annotation: V29 alignments GRCh38 3.1 GB link
ENCFF045TMO ENCFF045TMO.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 2.6 GB link
ENCFF139CPF ENCFF139CPF.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 2.2 GB link
ENCFF176YUC ENCFF176YUC.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 3.1 GB link
ENCFF605MVJ ENCFF605MVJ.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 2.7 GB link
ENCFF709JHZ ENCFF709JHZ.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 2.2 GB link
ENCFF763VDJ ENCFF763VDJ.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 2.6 GB link
ENCFF091MEF ENCFF091MEF.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V24 transcriptome alignments GRCh38 3.2 GB link
ENCFF726OOE ENCFF726OOE.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V24 transcriptome alignments GRCh38 3.7 GB link
ENCFF064SWO ENCFF064SWO.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V29 transcriptome alignments GRCh38 3.6 GB link
ENCFF489TBV ENCFF489TBV.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V29 transcriptome alignments GRCh38 4.2 GB link
ENCFF063CCK ENCFF063CCK.bam bam (transcriptome alignments); assembly: hg19; genome annotation: V19 transcriptome alignments hg19 3.1 GB link
ENCFF096XXP ENCFF096XXP.bam bam (transcriptome alignments); assembly: hg19; genome annotation: V19 transcriptome alignments hg19 3.7 GB link
ENCFF087HPN ENCFF087HPN.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 64.1 MB link
ENCFF122DRJ ENCFF122DRJ.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 59.4 MB link
ENCFF282QRU ENCFF282QRU.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 66.0 MB link
ENCFF320GTE ENCFF320GTE.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 70.9 MB link
ENCFF552OTS ENCFF552OTS.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V29 minus strand signal of all reads GRCh38 66.0 MB link
ENCFF945XYL ENCFF945XYL.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V29 minus strand signal of all reads GRCh38 71.0 MB link
ENCFF253ZEY ENCFF253ZEY.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 60.7 MB link
ENCFF500XQY ENCFF500XQY.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 64.7 MB link
ENCFF523MCV ENCFF523MCV.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 70.0 MB link
ENCFF566ILF ENCFF566ILF.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 55.9 MB link
ENCFF728OLO ENCFF728OLO.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 64.5 MB link
ENCFF874IWN ENCFF874IWN.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 59.5 MB link
ENCFF116IKL ENCFF116IKL.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 54.7 MB link
ENCFF134OCY ENCFF134OCY.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 62.1 MB link
ENCFF290EJL ENCFF290EJL.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 57.6 MB link
ENCFF630HBS ENCFF630HBS.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 59.6 MB link
ENCFF328ERS ENCFF328ERS.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 minus strand signal of unique reads GRCh38 62.8 MB link
ENCFF623IKY ENCFF623IKY.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 minus strand signal of unique reads GRCh38 57.7 MB link
ENCFF064BLM ENCFF064BLM.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 55.7 MB link
ENCFF309BED ENCFF309BED.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 59.4 MB link
ENCFF332BWZ ENCFF332BWZ.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 54.7 MB link
ENCFF818IVI ENCFF818IVI.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 58.0 MB link
ENCFF857DJH ENCFF857DJH.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 50.9 MB link
ENCFF872ZVI ENCFF872ZVI.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 62.3 MB link
ENCFF194MVC ENCFF194MVC.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 71.8 MB link
ENCFF279EMZ ENCFF279EMZ.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 66.7 MB link
ENCFF371NOW ENCFF371NOW.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 64.9 MB link
ENCFF937OBG ENCFF937OBG.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 60.1 MB link
ENCFF395JDP ENCFF395JDP.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V29 plus strand signal of all reads GRCh38 71.9 MB link
ENCFF492RUU ENCFF492RUU.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V29 plus strand signal of all reads GRCh38 66.7 MB link
ENCFF038CJZ ENCFF038CJZ.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 70.9 MB link
ENCFF073CLQ ENCFF073CLQ.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 60.5 MB link
ENCFF187ODB ENCFF187ODB.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 65.9 MB link
ENCFF566NGP ENCFF566NGP.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 65.2 MB link
ENCFF579MTC ENCFF579MTC.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 56.9 MB link
ENCFF589RJC ENCFF589RJC.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 61.9 MB link
ENCFF077QDO ENCFF077QDO.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 58.8 MB link
ENCFF098DMG ENCFF098DMG.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 63.6 MB link
ENCFF613FIO ENCFF613FIO.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 55.8 MB link
ENCFF767DTU ENCFF767DTU.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 60.9 MB link
ENCFF250ZFO ENCFF250ZFO.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 plus strand signal of unique reads GRCh38 58.9 MB link
ENCFF591YKJ ENCFF591YKJ.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 plus strand signal of unique reads GRCh38 64.3 MB link
ENCFF030BHE ENCFF030BHE.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 57.4 MB link
ENCFF446DMG ENCFF446DMG.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 52.4 MB link
ENCFF608LKD ENCFF608LKD.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 61.0 MB link
ENCFF730TZT ENCFF730TZT.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 59.3 MB link
ENCFF869AQN ENCFF869AQN.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 56.0 MB link
ENCFF946SHN ENCFF946SHN.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 64.0 MB link
ENCFF005GDQ ENCFF005GDQ.fastq fastq (reads) reads 1.8 GB link
ENCFF168MEE ENCFF168MEE.fastq fastq (reads) reads 1.4 GB link
ENCFF313JCV ENCFF313JCV.fastq fastq (reads) reads 1.6 GB link
ENCFF807JYP ENCFF807JYP.fastq fastq (reads) reads 1.5 GB link
ENCFF332XNP ENCFF332XNP.tar tar (differential splicing quantifications); assembly: hg19; genome annotation: V19 differential splicing quantifications hg19 2.8 MB link
ENCFF888JIH ENCFF888JIH.tar tar (differential splicing quantifications); assembly: hg19; genome annotation: V19 differential splicing quantifications hg19 3.1 MB link
ENCFF972IYR ENCFF972IYR.tar tar (differential splicing quantifications); assembly: hg19; genome annotation: V19 differential splicing quantifications hg19 12.9 MB link
ENCFF102SLI ENCFF102SLI.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 1.8 MB link
ENCFF132WOO ENCFF132WOO.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 4.1 MB link
ENCFF440VJX ENCFF440VJX.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 5.4 MB link
ENCFF585OXW ENCFF585OXW.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 2.8 MB link
ENCFF839OCI ENCFF839OCI.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 1.9 MB link
ENCFF153BJQ ENCFF153BJQ.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V24 gene quantifications GRCh38 9.4 MB link
ENCFF845BGZ ENCFF845BGZ.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V24 gene quantifications GRCh38 9.4 MB link
ENCFF492XIY ENCFF492XIY.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V29 gene quantifications GRCh38 10.4 MB link
ENCFF655EYM ENCFF655EYM.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V29 gene quantifications GRCh38 10.4 MB link
ENCFF732LKW ENCFF732LKW.tsv tsv (gene quantifications); assembly: hg19; genome annotation: V19 gene quantifications hg19 9.1 MB link
ENCFF817ERB ENCFF817ERB.tsv tsv (gene quantifications); assembly: hg19; genome annotation: V19 gene quantifications hg19 9.1 MB link
ENCFF353OKB ENCFF353OKB.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V24 transcript quantifications GRCh38 25.3 MB link
ENCFF987BKF ENCFF987BKF.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V24 transcript quantifications GRCh38 25.3 MB link
ENCFF471FAW ENCFF471FAW.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 29.8 MB link
ENCFF517REW ENCFF517REW.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 27.2 MB link
ENCFF708USI ENCFF708USI.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 29.8 MB link
ENCFF915LCA ENCFF915LCA.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 27.3 MB link
ENCFF028MDN ENCFF028MDN.tsv tsv (transcript quantifications); assembly: hg19; genome annotation: V19 transcript quantifications hg19 24.8 MB link
ENCFF351QJJ ENCFF351QJJ.tsv tsv (transcript quantifications); assembly: hg19; genome annotation: V19 transcript quantifications hg19 24.9 MB link