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ENCSR946OFN

ENCSR ENCODE
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shRNA knockdown against TROVE2 in HepG2 cells followed by RNA-seq. (TROVE2_BGHLV16)

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

Summary

shRNA RNA-seq of TROVE2 in Homo sapiens HepG2 expressing RNAi targeting H. sapiens TROVE2

Overall Design

shRNA knockdown against TROVE2 in HepG2 cells followed by RNA-seq. (TROVE2_BGHLV16)

Analysis

View Data Processing
Analysis page is available for ENCSR946OFN.

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: 55.5 GB
Assay: shRNA RNA-seq
Target: TROVE2
Biosample: Homo sapiens HepG2 expressing RNAi targeting H. sapiens TROVE2
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
ENCFF257DUD ENCFF257DUD.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 2.0 GB link
ENCFF772JIO ENCFF772JIO.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 2.4 GB link
ENCFF821MGJ ENCFF821MGJ.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 2.2 GB link
ENCFF940WWC ENCFF940WWC.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 2.6 GB link
ENCFF736AQS ENCFF736AQS.bam bam (alignments); assembly: GRCh38; genome annotation: V29 alignments GRCh38 2.4 GB link
ENCFF901UFY ENCFF901UFY.bam bam (alignments); assembly: GRCh38; genome annotation: V29 alignments GRCh38 2.6 GB link
ENCFF099TTE ENCFF099TTE.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 2.2 GB link
ENCFF101CEO ENCFF101CEO.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 2.0 GB link
ENCFF115CEE ENCFF115CEE.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 2.6 GB link
ENCFF119ZCG ENCFF119ZCG.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 2.4 GB link
ENCFF558UNB ENCFF558UNB.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 2.2 GB link
ENCFF565GTX ENCFF565GTX.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 2.0 GB link
ENCFF252IDD ENCFF252IDD.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V24 transcriptome alignments GRCh38 3.0 GB link
ENCFF727PEY ENCFF727PEY.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V24 transcriptome alignments GRCh38 3.3 GB link
ENCFF064NRZ ENCFF064NRZ.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V29 transcriptome alignments GRCh38 3.7 GB link
ENCFF855RTT ENCFF855RTT.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V29 transcriptome alignments GRCh38 3.4 GB link
ENCFF099NGA ENCFF099NGA.bam bam (transcriptome alignments); assembly: hg19; genome annotation: V19 transcriptome alignments hg19 3.3 GB link
ENCFF128RSC ENCFF128RSC.bam bam (transcriptome alignments); assembly: hg19; genome annotation: V19 transcriptome alignments hg19 3.0 GB link
ENCFF771NXR ENCFF771NXR.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 56.5 MB link
ENCFF849DWS ENCFF849DWS.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 50.2 MB link
ENCFF865HIP ENCFF865HIP.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 50.6 MB link
ENCFF876CMZ ENCFF876CMZ.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 55.7 MB link
ENCFF142NHW ENCFF142NHW.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V29 minus strand signal of all reads GRCh38 56.5 MB link
ENCFF692MME ENCFF692MME.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V29 minus strand signal of all reads GRCh38 55.7 MB link
ENCFF204HQD ENCFF204HQD.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 55.1 MB link
ENCFF257EHL ENCFF257EHL.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 51.5 MB link
ENCFF285ITB ENCFF285ITB.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 48.3 MB link
ENCFF486LUL ENCFF486LUL.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 50.9 MB link
ENCFF617VEE ENCFF617VEE.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 56.0 MB link
ENCFF890ZNO ENCFF890ZNO.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 49.2 MB link
ENCFF384REO ENCFF384REO.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 50.4 MB link
ENCFF413BXX ENCFF413BXX.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 47.6 MB link
ENCFF425MWW ENCFF425MWW.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 48.2 MB link
ENCFF696BXF ENCFF696BXF.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 49.7 MB link
ENCFF006HME ENCFF006HME.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 minus strand signal of unique reads GRCh38 50.5 MB link
ENCFF602TQV ENCFF602TQV.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 minus strand signal of unique reads GRCh38 50.3 MB link
ENCFF059EKP ENCFF059EKP.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 48.3 MB link
ENCFF102TKH ENCFF102TKH.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 45.7 MB link
ENCFF286BWN ENCFF286BWN.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 44.7 MB link
ENCFF479UPC ENCFF479UPC.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 47.8 MB link
ENCFF491JWH ENCFF491JWH.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 50.2 MB link
ENCFF821TUP ENCFF821TUP.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 50.8 MB link
ENCFF103RNM ENCFF103RNM.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 51.2 MB link
ENCFF590RCK ENCFF590RCK.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 57.6 MB link
ENCFF863LGX ENCFF863LGX.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 56.8 MB link
ENCFF999XIF ENCFF999XIF.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 51.5 MB link
ENCFF361TTG ENCFF361TTG.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V29 plus strand signal of all reads GRCh38 57.6 MB link
ENCFF748MKW ENCFF748MKW.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V29 plus strand signal of all reads GRCh38 56.8 MB link
ENCFF163BXI ENCFF163BXI.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 50.3 MB link
ENCFF395URL ENCFF395URL.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 57.0 MB link
ENCFF418QKV ENCFF418QKV.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 52.6 MB link
ENCFF626LVX ENCFF626LVX.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 56.0 MB link
ENCFF683PNY ENCFF683PNY.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 52.0 MB link
ENCFF713RJU ENCFF713RJU.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 49.4 MB link
ENCFF096PYQ ENCFF096PYQ.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 49.3 MB link
ENCFF220MSN ENCFF220MSN.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 48.8 MB link
ENCFF276PMY ENCFF276PMY.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 51.7 MB link
ENCFF545RCZ ENCFF545RCZ.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 51.0 MB link
ENCFF703VHW ENCFF703VHW.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 plus strand signal of unique reads GRCh38 51.8 MB link
ENCFF778GXB ENCFF778GXB.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 plus strand signal of unique reads GRCh38 51.6 MB link
ENCFF171OWJ ENCFF171OWJ.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 52.2 MB link
ENCFF573RJG ENCFF573RJG.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 49.1 MB link
ENCFF647XZS ENCFF647XZS.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 47.1 MB link
ENCFF688ROD ENCFF688ROD.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 51.6 MB link
ENCFF703EMC ENCFF703EMC.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 46.0 MB link
ENCFF776AUD ENCFF776AUD.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 49.6 MB link
ENCFF233IZY ENCFF233IZY.fastq fastq (reads) reads 1.4 GB link
ENCFF278WVM ENCFF278WVM.fastq fastq (reads) reads 1.5 GB link
ENCFF773TIP ENCFF773TIP.fastq fastq (reads) reads 1.3 GB link
ENCFF992YHM ENCFF992YHM.fastq fastq (reads) reads 1.3 GB link
ENCFF045NJQ ENCFF045NJQ.tar tar (differential splicing quantifications); assembly: hg19; genome annotation: V19 differential splicing quantifications hg19 12.8 MB link
ENCFF265CRF ENCFF265CRF.tar tar (differential splicing quantifications); assembly: hg19; genome annotation: V19 differential splicing quantifications hg19 2.6 MB link
ENCFF634QDI ENCFF634QDI.tar tar (differential splicing quantifications); assembly: hg19; genome annotation: V19 differential splicing quantifications hg19 2.9 MB link
ENCFF030TUO ENCFF030TUO.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 5.6 MB link
ENCFF053EYO ENCFF053EYO.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 4.1 MB link
ENCFF160LSJ ENCFF160LSJ.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 2.7 MB link
ENCFF464SMQ ENCFF464SMQ.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 1.9 MB link
ENCFF724LKK ENCFF724LKK.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 1.8 MB link
ENCFF616GGV ENCFF616GGV.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V24 gene quantifications GRCh38 9.4 MB link
ENCFF945REE ENCFF945REE.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V24 gene quantifications GRCh38 9.4 MB link
ENCFF082XEF ENCFF082XEF.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V29 gene quantifications GRCh38 10.4 MB link
ENCFF598CPJ ENCFF598CPJ.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V29 gene quantifications GRCh38 10.4 MB link
ENCFF427RKG ENCFF427RKG.tsv tsv (gene quantifications); assembly: hg19; genome annotation: V19 gene quantifications hg19 9.1 MB link
ENCFF496SSR ENCFF496SSR.tsv tsv (gene quantifications); assembly: hg19; genome annotation: V19 gene quantifications hg19 9.1 MB link
ENCFF631SLY ENCFF631SLY.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V24 transcript quantifications GRCh38 25.3 MB link
ENCFF867TEV ENCFF867TEV.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V24 transcript quantifications GRCh38 25.2 MB link
ENCFF095BZX ENCFF095BZX.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 27.2 MB link
ENCFF380WJD ENCFF380WJD.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 29.7 MB link
ENCFF453PBE ENCFF453PBE.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 27.2 MB link
ENCFF950USC ENCFF950USC.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 29.7 MB link
ENCFF073KMT ENCFF073KMT.tsv tsv (transcript quantifications); assembly: hg19; genome annotation: V19 transcript quantifications hg19 24.8 MB link
ENCFF202YYQ ENCFF202YYQ.tsv tsv (transcript quantifications); assembly: hg19; genome annotation: V19 transcript quantifications hg19 24.9 MB link