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ENCSR028YAQ

ENCSR ENCODE
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shRNA knockdown against PA2G4 in HepG2 cells followed by RNA-seq. (PA2G4_BGHLV16)

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

Summary

shRNA RNA-seq of PA2G4 in Homo sapiens HepG2 expressing RNAi targeting H. sapiens PA2G4

Overall Design

shRNA knockdown against PA2G4 in HepG2 cells followed by RNA-seq. (PA2G4_BGHLV16)

Analysis

View Data Processing
Analysis page is available for ENCSR028YAQ.

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: 54.1 GB
Assay: shRNA RNA-seq
Target: PA2G4
Biosample: Homo sapiens HepG2 expressing RNAi targeting H. sapiens PA2G4
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
ENCFF244ZQM ENCFF244ZQM.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 2.9 GB link
ENCFF477DPL ENCFF477DPL.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 2.4 GB link
ENCFF724ATS ENCFF724ATS.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 1.7 GB link
ENCFF889FRC ENCFF889FRC.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 2.1 GB link
ENCFF348PUN ENCFF348PUN.bam bam (alignments); assembly: GRCh38; genome annotation: V29 alignments GRCh38 2.1 GB link
ENCFF865AIP ENCFF865AIP.bam bam (alignments); assembly: GRCh38; genome annotation: V29 alignments GRCh38 2.9 GB link
ENCFF035FYR ENCFF035FYR.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 2.3 GB link
ENCFF136SOB ENCFF136SOB.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 2.0 GB link
ENCFF148JEE ENCFF148JEE.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 1.7 GB link
ENCFF182IIF ENCFF182IIF.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 1.7 GB link
ENCFF393QIH ENCFF393QIH.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 2.3 GB link
ENCFF687LTL ENCFF687LTL.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 2.8 GB link
ENCFF713NEI ENCFF713NEI.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V24 transcriptome alignments GRCh38 3.6 GB link
ENCFF939NBX ENCFF939NBX.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V24 transcriptome alignments GRCh38 2.6 GB link
ENCFF018RYB ENCFF018RYB.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V29 transcriptome alignments GRCh38 4.0 GB link
ENCFF844WBX ENCFF844WBX.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V29 transcriptome alignments GRCh38 2.9 GB link
ENCFF527HEM ENCFF527HEM.bam bam (transcriptome alignments); assembly: hg19; genome annotation: V19 transcriptome alignments hg19 3.5 GB link
ENCFF906KJE ENCFF906KJE.bam bam (transcriptome alignments); assembly: hg19; genome annotation: V19 transcriptome alignments hg19 2.6 GB link
ENCFF106RME ENCFF106RME.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 49.8 MB link
ENCFF109VNU ENCFF109VNU.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 48.3 MB link
ENCFF178BUK ENCFF178BUK.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 53.2 MB link
ENCFF843LEY ENCFF843LEY.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 44.7 MB link
ENCFF446TDD ENCFF446TDD.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V29 minus strand signal of all reads GRCh38 53.2 MB link
ENCFF461DKH ENCFF461DKH.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V29 minus strand signal of all reads GRCh38 49.9 MB link
ENCFF133TJJ ENCFF133TJJ.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 49.6 MB link
ENCFF167TOA ENCFF167TOA.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 53.3 MB link
ENCFF187SKE ENCFF187SKE.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 45.9 MB link
ENCFF211YPN ENCFF211YPN.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 42.4 MB link
ENCFF638PWV ENCFF638PWV.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 44.7 MB link
ENCFF800ICF ENCFF800ICF.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 48.8 MB link
ENCFF100XVC ENCFF100XVC.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 43.7 MB link
ENCFF446TUT ENCFF446TUT.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 48.6 MB link
ENCFF535HIV ENCFF535HIV.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 42.5 MB link
ENCFF805JPH ENCFF805JPH.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 45.1 MB link
ENCFF729QNS ENCFF729QNS.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 minus strand signal of unique reads GRCh38 43.6 MB link
ENCFF976ZHM ENCFF976ZHM.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 minus strand signal of unique reads GRCh38 48.3 MB link
ENCFF339XSE ENCFF339XSE.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 41.9 MB link
ENCFF347ZNK ENCFF347ZNK.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 44.1 MB link
ENCFF371FSO ENCFF371FSO.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 48.5 MB link
ENCFF596LWP ENCFF596LWP.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 43.5 MB link
ENCFF653TEU ENCFF653TEU.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 46.0 MB link
ENCFF953PNN ENCFF953PNN.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 39.2 MB link
ENCFF165HYL ENCFF165HYL.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 49.5 MB link
ENCFF331CNP ENCFF331CNP.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 50.9 MB link
ENCFF794OWP ENCFF794OWP.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 45.7 MB link
ENCFF963GHH ENCFF963GHH.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 54.6 MB link
ENCFF319IZD ENCFF319IZD.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V29 plus strand signal of all reads GRCh38 51.0 MB link
ENCFF553DSY ENCFF553DSY.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V29 plus strand signal of all reads GRCh38 54.6 MB link
ENCFF034YPV ENCFF034YPV.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 47.2 MB link
ENCFF105FFH ENCFF105FFH.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 54.5 MB link
ENCFF328XMG ENCFF328XMG.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 50.5 MB link
ENCFF785HIZ ENCFF785HIZ.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 45.6 MB link
ENCFF802HRV ENCFF802HRV.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 50.0 MB link
ENCFF836ELC ENCFF836ELC.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 43.5 MB link
ENCFF105NIM ENCFF105NIM.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 50.0 MB link
ENCFF538IRT ENCFF538IRT.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 43.5 MB link
ENCFF681WRB ENCFF681WRB.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 44.9 MB link
ENCFF889IEM ENCFF889IEM.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 46.3 MB link
ENCFF037ZJQ ENCFF037ZJQ.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 plus strand signal of unique reads GRCh38 44.8 MB link
ENCFF049HNJ ENCFF049HNJ.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 plus strand signal of unique reads GRCh38 49.7 MB link
ENCFF165DFJ ENCFF165DFJ.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 40.3 MB link
ENCFF175EXB ENCFF175EXB.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 45.3 MB link
ENCFF232DNW ENCFF232DNW.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 43.1 MB link
ENCFF351WKY ENCFF351WKY.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 47.4 MB link
ENCFF488XHN ENCFF488XHN.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 49.9 MB link
ENCFF514WEH ENCFF514WEH.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 45.0 MB link
ENCFF060ZTX ENCFF060ZTX.fastq fastq (reads) reads 1.2 GB link
ENCFF061LWF ENCFF061LWF.fastq fastq (reads) reads 1.5 GB link
ENCFF519JRM ENCFF519JRM.fastq fastq (reads) reads 1.1 GB link
ENCFF555DRB ENCFF555DRB.fastq fastq (reads) reads 1.6 GB link
ENCFF149CUO ENCFF149CUO.tar tar (differential splicing quantifications); assembly: hg19; genome annotation: V19 differential splicing quantifications hg19 2.5 MB link
ENCFF449TPO ENCFF449TPO.tar tar (differential splicing quantifications); assembly: hg19; genome annotation: V19 differential splicing quantifications hg19 12.3 MB link
ENCFF911BRX ENCFF911BRX.tar tar (differential splicing quantifications); assembly: hg19; genome annotation: V19 differential splicing quantifications hg19 2.9 MB link
ENCFF028RGS ENCFF028RGS.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 5.5 MB link
ENCFF306AVY ENCFF306AVY.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 4.1 MB link
ENCFF548DNF ENCFF548DNF.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 1.8 MB link
ENCFF587HWF ENCFF587HWF.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 1.9 MB link
ENCFF972LYY ENCFF972LYY.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 2.7 MB link
ENCFF446UPJ ENCFF446UPJ.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V24 gene quantifications GRCh38 9.4 MB link
ENCFF578JQC ENCFF578JQC.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V24 gene quantifications GRCh38 9.4 MB link
ENCFF442ATY ENCFF442ATY.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V29 gene quantifications GRCh38 10.4 MB link
ENCFF801LSC ENCFF801LSC.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V29 gene quantifications GRCh38 10.4 MB link
ENCFF441MEE ENCFF441MEE.tsv tsv (gene quantifications); assembly: hg19; genome annotation: V19 gene quantifications hg19 9.1 MB link
ENCFF914YMY ENCFF914YMY.tsv tsv (gene quantifications); assembly: hg19; genome annotation: V19 gene quantifications hg19 9.1 MB link
ENCFF288IQC ENCFF288IQC.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V24 transcript quantifications GRCh38 25.2 MB link
ENCFF874EMG ENCFF874EMG.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V24 transcript quantifications GRCh38 25.3 MB link
ENCFF150AQN ENCFF150AQN.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 27.2 MB link
ENCFF236QEN ENCFF236QEN.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 27.2 MB link
ENCFF486PSG ENCFF486PSG.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 29.7 MB link
ENCFF874DDJ ENCFF874DDJ.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 29.8 MB link
ENCFF149PPM ENCFF149PPM.tsv tsv (transcript quantifications); assembly: hg19; genome annotation: V19 transcript quantifications hg19 24.8 MB link
ENCFF786BQC ENCFF786BQC.tsv tsv (transcript quantifications); assembly: hg19; genome annotation: V19 transcript quantifications hg19 24.9 MB link