← All datasets

ENCSR081IAO

ENCSR ENCODE
Export SRA CSV View on ENCODE

RNA-seq on HepG2 cells treated with an shRNA knockdown against CCAR1. (CCAR1_BGHLV20)

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

Summary

shRNA RNA-seq of CCAR1 in Homo sapiens HepG2 expressing RNAi targeting H. sapiens CCAR1

Overall Design

RNA-seq on HepG2 cells treated with an shRNA knockdown against CCAR1. (CCAR1_BGHLV20)

Analysis

View Data Processing
Analysis page is available for ENCSR081IAO.

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: 147.2 GB
Assay: shRNA RNA-seq
Target: CCAR1
Biosample: Homo sapiens HepG2 expressing RNAi targeting H. sapiens CCAR1
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
ENCFF169UXZ ENCFF169UXZ.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 7.3 GB link
ENCFF746LSF ENCFF746LSF.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 7.1 GB link
ENCFF942OUY ENCFF942OUY.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 6.0 GB link
ENCFF963WSB ENCFF963WSB.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 5.9 GB link
ENCFF409TFG ENCFF409TFG.bam bam (alignments); assembly: GRCh38; genome annotation: V29 alignments GRCh38 7.1 GB link
ENCFF868KOZ ENCFF868KOZ.bam bam (alignments); assembly: GRCh38; genome annotation: V29 alignments GRCh38 7.3 GB link
ENCFF396LJX ENCFF396LJX.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 5.7 GB link
ENCFF654XYV ENCFF654XYV.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 5.7 GB link
ENCFF815IWS ENCFF815IWS.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 5.9 GB link
ENCFF874TAD ENCFF874TAD.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 6.8 GB link
ENCFF900XSL ENCFF900XSL.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 5.9 GB link
ENCFF981UXB ENCFF981UXB.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 7.0 GB link
ENCFF131PVU ENCFF131PVU.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V24 transcriptome alignments GRCh38 7.8 GB link
ENCFF541DSW ENCFF541DSW.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V24 transcriptome alignments GRCh38 8.0 GB link
ENCFF449PGH ENCFF449PGH.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V29 transcriptome alignments GRCh38 8.8 GB link
ENCFF619ZWW ENCFF619ZWW.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V29 transcriptome alignments GRCh38 9.0 GB link
ENCFF223TWR ENCFF223TWR.bam bam (transcriptome alignments); assembly: hg19; genome annotation: V19 transcriptome alignments hg19 8.0 GB link
ENCFF518KSC ENCFF518KSC.bam bam (transcriptome alignments); assembly: hg19; genome annotation: V19 transcriptome alignments hg19 7.8 GB link
ENCFF565HOR ENCFF565HOR.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 94.6 MB link
ENCFF815JNC ENCFF815JNC.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 110.7 MB link
ENCFF815YPH ENCFF815YPH.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 92.4 MB link
ENCFF840HIV ENCFF840HIV.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 107.9 MB link
ENCFF485NVW ENCFF485NVW.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V29 minus strand signal of all reads GRCh38 110.8 MB link
ENCFF850LPJ ENCFF850LPJ.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V29 minus strand signal of all reads GRCh38 107.9 MB link
ENCFF429NUD ENCFF429NUD.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 93.0 MB link
ENCFF628FXA ENCFF628FXA.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 108.0 MB link
ENCFF699UBW ENCFF699UBW.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 94.0 MB link
ENCFF777JYI ENCFF777JYI.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 96.0 MB link
ENCFF938TRS ENCFF938TRS.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 109.8 MB link
ENCFF954ZON ENCFF954ZON.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 91.5 MB link
ENCFF122RLU ENCFF122RLU.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 88.4 MB link
ENCFF193KQG ENCFF193KQG.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 96.6 MB link
ENCFF270QWJ ENCFF270QWJ.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 96.9 MB link
ENCFF421SIJ ENCFF421SIJ.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 86.4 MB link
ENCFF260SZX ENCFF260SZX.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 minus strand signal of unique reads GRCh38 96.5 MB link
ENCFF781ZDK ENCFF781ZDK.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 minus strand signal of unique reads GRCh38 97.2 MB link
ENCFF293TBF ENCFF293TBF.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 85.1 MB link
ENCFF482LZV ENCFF482LZV.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 88.3 MB link
ENCFF742DLM ENCFF742DLM.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 84.0 MB link
ENCFF750NYO ENCFF750NYO.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 89.0 MB link
ENCFF827ITH ENCFF827ITH.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 98.1 MB link
ENCFF852NEH ENCFF852NEH.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 96.5 MB link
ENCFF198DFL ENCFF198DFL.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 113.3 MB link
ENCFF433FYO ENCFF433FYO.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 96.9 MB link
ENCFF460DQR ENCFF460DQR.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 110.5 MB link
ENCFF761BXL ENCFF761BXL.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 94.6 MB link
ENCFF061FOP ENCFF061FOP.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V29 plus strand signal of all reads GRCh38 113.3 MB link
ENCFF603RFD ENCFF603RFD.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V29 plus strand signal of all reads GRCh38 110.5 MB link
ENCFF137TTO ENCFF137TTO.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 93.9 MB link
ENCFF161UGN ENCFF161UGN.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 112.1 MB link
ENCFF302PEA ENCFF302PEA.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 98.5 MB link
ENCFF765IAU ENCFF765IAU.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 95.4 MB link
ENCFF790LNN ENCFF790LNN.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 96.4 MB link
ENCFF897EXI ENCFF897EXI.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 110.4 MB link
ENCFF341VOT ENCFF341VOT.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 100.1 MB link
ENCFF362RDT ENCFF362RDT.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 99.9 MB link
ENCFF478KLQ ENCFF478KLQ.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 91.2 MB link
ENCFF552YIQ ENCFF552YIQ.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 89.1 MB link
ENCFF414NOO ENCFF414NOO.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 plus strand signal of unique reads GRCh38 99.8 MB link
ENCFF874ITW ENCFF874ITW.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 plus strand signal of unique reads GRCh38 100.3 MB link
ENCFF154XLM ENCFF154XLM.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 91.3 MB link
ENCFF563XGW ENCFF563XGW.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 101.4 MB link
ENCFF677BUJ ENCFF677BUJ.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 99.8 MB link
ENCFF767MOL ENCFF767MOL.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 88.0 MB link
ENCFF964BMT ENCFF964BMT.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 86.8 MB link
ENCFF991JKJ ENCFF991JKJ.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 92.0 MB link
ENCFF185OKC ENCFF185OKC.fastq fastq (reads) reads 3.7 GB link
ENCFF211JML ENCFF211JML.fastq fastq (reads) reads 3.9 GB link
ENCFF603MKL ENCFF603MKL.fastq fastq (reads) reads 3.8 GB link
ENCFF642WHU ENCFF642WHU.fastq fastq (reads) reads 3.7 GB link
ENCFF330YBG ENCFF330YBG.tar tar (differential splicing quantifications); assembly: hg19; genome annotation: V19 differential splicing quantifications hg19 3.6 MB link
ENCFF533GAE ENCFF533GAE.tar tar (differential splicing quantifications); assembly: hg19; genome annotation: V19 differential splicing quantifications hg19 4.5 MB link
ENCFF972JBH ENCFF972JBH.tar tar (differential splicing quantifications); assembly: hg19; genome annotation: V19 differential splicing quantifications hg19 18.0 MB link
ENCFF331MUY ENCFF331MUY.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 3.0 MB link
ENCFF635KLH ENCFF635KLH.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 1.7 MB link
ENCFF867WSE ENCFF867WSE.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 5.6 MB link
ENCFF896SNX ENCFF896SNX.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 4.4 MB link
ENCFF898ENN ENCFF898ENN.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 2.0 MB link
ENCFF331ILS ENCFF331ILS.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V24 gene quantifications GRCh38 9.5 MB link
ENCFF758CIJ ENCFF758CIJ.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V24 gene quantifications GRCh38 9.5 MB link
ENCFF542WTQ ENCFF542WTQ.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V29 gene quantifications GRCh38 10.4 MB link
ENCFF867FSM ENCFF867FSM.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V29 gene quantifications GRCh38 10.4 MB link
ENCFF400OWQ ENCFF400OWQ.tsv tsv (gene quantifications); assembly: hg19; genome annotation: V19 gene quantifications hg19 9.1 MB link
ENCFF817EIQ ENCFF817EIQ.tsv tsv (gene quantifications); assembly: hg19; genome annotation: V19 gene quantifications hg19 9.1 MB link
ENCFF061ACX ENCFF061ACX.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V24 transcript quantifications GRCh38 25.3 MB link
ENCFF376SOX ENCFF376SOX.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V24 transcript quantifications GRCh38 25.3 MB link
ENCFF282EMI ENCFF282EMI.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 27.5 MB link
ENCFF616SZW ENCFF616SZW.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 27.5 MB link
ENCFF635SDV ENCFF635SDV.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 29.8 MB link
ENCFF757WTF ENCFF757WTF.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 29.8 MB link
ENCFF320YEW ENCFF320YEW.tsv tsv (transcript quantifications); assembly: hg19; genome annotation: V19 transcript quantifications hg19 24.9 MB link
ENCFF329ESD ENCFF329ESD.tsv tsv (transcript quantifications); assembly: hg19; genome annotation: V19 transcript quantifications hg19 24.9 MB link