← All datasets

ENCSR481AYC

ENCSR ENCODE
Export SRA CSV View on ENCODE

shRNA knockdown against BCLAF1 in HepG2 cells followed by RNA-seq. (BCLAF1_BGHLV17)

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

Summary

shRNA RNA-seq of BCLAF1 in Homo sapiens HepG2 expressing RNAi targeting H. sapiens BCLAF1

Overall Design

shRNA knockdown against BCLAF1 in HepG2 cells followed by RNA-seq. (BCLAF1_BGHLV17)

Analysis

View Data Processing
Analysis page is available for ENCSR481AYC.

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: 111.3 GB
Assay: shRNA RNA-seq
Target: BCLAF1
Biosample: Homo sapiens HepG2 expressing RNAi targeting H. sapiens BCLAF1
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
ENCFF101BXP ENCFF101BXP.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 4.3 GB link
ENCFF183JNZ ENCFF183JNZ.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 3.6 GB link
ENCFF919OFB ENCFF919OFB.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 6.1 GB link
ENCFF987VHQ ENCFF987VHQ.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 5.1 GB link
ENCFF066CDX ENCFF066CDX.bam bam (alignments); assembly: GRCh38; genome annotation: V29 alignments GRCh38 6.1 GB link
ENCFF986DTN ENCFF986DTN.bam bam (alignments); assembly: GRCh38; genome annotation: V29 alignments GRCh38 4.3 GB link
ENCFF254QYF ENCFF254QYF.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 3.6 GB link
ENCFF411XAT ENCFF411XAT.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 5.1 GB link
ENCFF587FCY ENCFF587FCY.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 4.2 GB link
ENCFF775APS ENCFF775APS.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 5.1 GB link
ENCFF808MJW ENCFF808MJW.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 3.5 GB link
ENCFF878AAZ ENCFF878AAZ.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 5.9 GB link
ENCFF473MUQ ENCFF473MUQ.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V24 transcriptome alignments GRCh38 5.1 GB link
ENCFF869QXC ENCFF869QXC.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V24 transcriptome alignments GRCh38 7.4 GB link
ENCFF312HWG ENCFF312HWG.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V29 transcriptome alignments GRCh38 5.8 GB link
ENCFF404XJJ ENCFF404XJJ.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V29 transcriptome alignments GRCh38 8.3 GB link
ENCFF181XKF ENCFF181XKF.bam bam (transcriptome alignments); assembly: hg19; genome annotation: V19 transcriptome alignments hg19 5.1 GB link
ENCFF644ZQS ENCFF644ZQS.bam bam (transcriptome alignments); assembly: hg19; genome annotation: V19 transcriptome alignments hg19 7.3 GB link
ENCFF322KLK ENCFF322KLK.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 81.9 MB link
ENCFF405KRF ENCFF405KRF.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 95.1 MB link
ENCFF559JUE ENCFF559JUE.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 85.3 MB link
ENCFF823DVX ENCFF823DVX.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 72.5 MB link
ENCFF138OJE ENCFF138OJE.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V29 minus strand signal of all reads GRCh38 81.8 MB link
ENCFF267JVY ENCFF267JVY.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V29 minus strand signal of all reads GRCh38 95.2 MB link
ENCFF052SPD ENCFF052SPD.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 94.7 MB link
ENCFF261KWZ ENCFF261KWZ.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 73.5 MB link
ENCFF483JFK ENCFF483JFK.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 83.4 MB link
ENCFF598PKV ENCFF598PKV.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 87.5 MB link
ENCFF647TRN ENCFF647TRN.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 81.2 MB link
ENCFF817YDZ ENCFF817YDZ.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 69.7 MB link
ENCFF452EII ENCFF452EII.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 85.2 MB link
ENCFF710NNY ENCFF710NNY.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 73.1 MB link
ENCFF844IIU ENCFF844IIU.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 80.5 MB link
ENCFF863BLM ENCFF863BLM.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 68.4 MB link
ENCFF073LPD ENCFF073LPD.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 minus strand signal of unique reads GRCh38 85.7 MB link
ENCFF905LZH ENCFF905LZH.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 minus strand signal of unique reads GRCh38 73.6 MB link
ENCFF111ZXQ ENCFF111ZXQ.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 85.6 MB link
ENCFF211AXG ENCFF211AXG.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 73.0 MB link
ENCFF259HJO ENCFF259HJO.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 80.5 MB link
ENCFF314ABD ENCFF314ABD.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 77.6 MB link
ENCFF411RMW ENCFF411RMW.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 68.5 MB link
ENCFF560RLJ ENCFF560RLJ.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 65.2 MB link
ENCFF288XGN ENCFF288XGN.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 87.0 MB link
ENCFF609PLJ ENCFF609PLJ.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 97.0 MB link
ENCFF917CAD ENCFF917CAD.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 73.9 MB link
ENCFF934MCA ENCFF934MCA.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 83.5 MB link
ENCFF154XRY ENCFF154XRY.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V29 plus strand signal of all reads GRCh38 97.1 MB link
ENCFF359UWT ENCFF359UWT.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V29 plus strand signal of all reads GRCh38 83.4 MB link
ENCFF113BHI ENCFF113BHI.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 85.5 MB link
ENCFF128EJX ENCFF128EJX.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 96.4 MB link
ENCFF348RQO ENCFF348RQO.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 75.0 MB link
ENCFF793JSM ENCFF793JSM.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 71.4 MB link
ENCFF878PXO ENCFF878PXO.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 82.6 MB link
ENCFF907ZHY ENCFF907ZHY.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 89.4 MB link
ENCFF002JTH ENCFF002JTH.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 87.6 MB link
ENCFF141MCE ENCFF141MCE.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 82.7 MB link
ENCFF264GJC ENCFF264GJC.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 75.1 MB link
ENCFF492JFQ ENCFF492JFQ.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 70.1 MB link
ENCFF495WOT ENCFF495WOT.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 plus strand signal of unique reads GRCh38 88.2 MB link
ENCFF796HSI ENCFF796HSI.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 plus strand signal of unique reads GRCh38 75.6 MB link
ENCFF182MIO ENCFF182MIO.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 88.2 MB link
ENCFF390DDW ENCFF390DDW.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 70.4 MB link
ENCFF444HVT ENCFF444HVT.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 67.2 MB link
ENCFF603MQB ENCFF603MQB.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 75.1 MB link
ENCFF701IVM ENCFF701IVM.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 80.2 MB link
ENCFF904VNU ENCFF904VNU.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 82.9 MB link
ENCFF132GHM ENCFF132GHM.fastq fastq (reads) reads 2.3 GB link
ENCFF182RAD ENCFF182RAD.fastq fastq (reads) reads 3.4 GB link
ENCFF267DZP ENCFF267DZP.fastq fastq (reads) reads 2.3 GB link
ENCFF863SFE ENCFF863SFE.fastq fastq (reads) reads 3.2 GB link
ENCFF554SSE ENCFF554SSE.tar tar (differential splicing quantifications); assembly: hg19; genome annotation: V19 differential splicing quantifications hg19 3.9 MB link
ENCFF644KIX ENCFF644KIX.tar tar (differential splicing quantifications); assembly: hg19; genome annotation: V19 differential splicing quantifications hg19 3.2 MB link
ENCFF736OUK ENCFF736OUK.tar tar (differential splicing quantifications); assembly: hg19; genome annotation: V19 differential splicing quantifications hg19 16.0 MB link
ENCFF325FNG ENCFF325FNG.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 1.8 MB link
ENCFF397SJD ENCFF397SJD.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 2.0 MB link
ENCFF497BSV ENCFF497BSV.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 4.3 MB link
ENCFF773MUK ENCFF773MUK.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 2.9 MB link
ENCFF989BIT ENCFF989BIT.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 5.6 MB link
ENCFF580GPY ENCFF580GPY.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V24 gene quantifications GRCh38 9.4 MB link
ENCFF842ZZW ENCFF842ZZW.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V24 gene quantifications GRCh38 9.4 MB link
ENCFF395WSF ENCFF395WSF.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V29 gene quantifications GRCh38 10.4 MB link
ENCFF773IOD ENCFF773IOD.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V29 gene quantifications GRCh38 10.4 MB link
ENCFF670VTV ENCFF670VTV.tsv tsv (gene quantifications); assembly: hg19; genome annotation: V19 gene quantifications hg19 9.1 MB link
ENCFF881ZZE ENCFF881ZZE.tsv tsv (gene quantifications); assembly: hg19; genome annotation: V19 gene quantifications hg19 9.1 MB link
ENCFF192RKD ENCFF192RKD.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V24 transcript quantifications GRCh38 25.3 MB link
ENCFF769SDH ENCFF769SDH.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V24 transcript quantifications GRCh38 25.3 MB link
ENCFF161VPC ENCFF161VPC.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 27.4 MB link
ENCFF400LQQ ENCFF400LQQ.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 27.3 MB link
ENCFF857WVF ENCFF857WVF.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 29.8 MB link
ENCFF977TDX ENCFF977TDX.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 29.8 MB link
ENCFF270ZJS ENCFF270ZJS.tsv tsv (transcript quantifications); assembly: hg19; genome annotation: V19 transcript quantifications hg19 24.9 MB link
ENCFF436CFX ENCFF436CFX.tsv tsv (transcript quantifications); assembly: hg19; genome annotation: V19 transcript quantifications hg19 24.9 MB link