← All datasets

ENCSR347ZHQ

ENCSR ENCODE
Export SRA CSV View on ENCODE

shRNA knockdown against XRN2 in HepG2 cells followed by RNA-seq. (XRN2_BGHLV17)

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

Summary

shRNA RNA-seq of XRN2 in Homo sapiens HepG2 expressing RNAi targeting H. sapiens XRN2

Overall Design

shRNA knockdown against XRN2 in HepG2 cells followed by RNA-seq. (XRN2_BGHLV17)

Analysis

View Data Processing
Analysis page is available for ENCSR347ZHQ.

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: XRN2
Biosample: Homo sapiens HepG2 expressing RNAi targeting H. sapiens XRN2
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
ENCFF002RWS ENCFF002RWS.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 5.0 GB link
ENCFF064TWV ENCFF064TWV.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 4.2 GB link
ENCFF619EBQ ENCFF619EBQ.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 5.1 GB link
ENCFF686OAP ENCFF686OAP.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 4.2 GB link
ENCFF804TFF ENCFF804TFF.bam bam (alignments); assembly: GRCh38; genome annotation: V29 alignments GRCh38 5.0 GB link
ENCFF958VEJ ENCFF958VEJ.bam bam (alignments); assembly: GRCh38; genome annotation: V29 alignments GRCh38 5.1 GB link
ENCFF226WWD ENCFF226WWD.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 4.2 GB link
ENCFF322LTW ENCFF322LTW.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 4.2 GB link
ENCFF407VNE ENCFF407VNE.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 4.2 GB link
ENCFF450HWR ENCFF450HWR.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 5.0 GB link
ENCFF458IUV ENCFF458IUV.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 4.2 GB link
ENCFF789QEA ENCFF789QEA.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 5.0 GB link
ENCFF291QGZ ENCFF291QGZ.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V24 transcriptome alignments GRCh38 6.6 GB link
ENCFF593JJK ENCFF593JJK.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V24 transcriptome alignments GRCh38 6.5 GB link
ENCFF047LJT ENCFF047LJT.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V29 transcriptome alignments GRCh38 7.4 GB link
ENCFF699FOP ENCFF699FOP.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V29 transcriptome alignments GRCh38 7.3 GB link
ENCFF213VTI ENCFF213VTI.bam bam (transcriptome alignments); assembly: hg19; genome annotation: V19 transcriptome alignments hg19 6.4 GB link
ENCFF332ZNI ENCFF332ZNI.bam bam (transcriptome alignments); assembly: hg19; genome annotation: V19 transcriptome alignments hg19 6.5 GB link
ENCFF195DTQ ENCFF195DTQ.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 83.7 MB link
ENCFF311KCE ENCFF311KCE.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 77.0 MB link
ENCFF808XVB ENCFF808XVB.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 76.7 MB link
ENCFF870CHU ENCFF870CHU.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 84.7 MB link
ENCFF511EKA ENCFF511EKA.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V29 minus strand signal of all reads GRCh38 83.7 MB link
ENCFF686CBM ENCFF686CBM.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V29 minus strand signal of all reads GRCh38 84.7 MB link
ENCFF007GIH ENCFF007GIH.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 83.9 MB link
ENCFF135JNM ENCFF135JNM.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 77.8 MB link
ENCFF147IIW ENCFF147IIW.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 74.6 MB link
ENCFF309BOB ENCFF309BOB.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 75.6 MB link
ENCFF395QWY ENCFF395QWY.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 83.8 MB link
ENCFF963FQG ENCFF963FQG.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 78.1 MB link
ENCFF072DRB ENCFF072DRB.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 76.8 MB link
ENCFF496SJF ENCFF496SJF.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 76.4 MB link
ENCFF673KHB ENCFF673KHB.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 72.5 MB link
ENCFF954PMX ENCFF954PMX.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 72.0 MB link
ENCFF633QXY ENCFF633QXY.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 minus strand signal of unique reads GRCh38 76.8 MB link
ENCFF945MJG ENCFF945MJG.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 minus strand signal of unique reads GRCh38 76.4 MB link
ENCFF185KWL ENCFF185KWL.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 72.6 MB link
ENCFF213AJJ ENCFF213AJJ.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 72.2 MB link
ENCFF358RSR ENCFF358RSR.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 76.7 MB link
ENCFF413QRU ENCFF413QRU.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 70.3 MB link
ENCFF680CMV ENCFF680CMV.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 70.3 MB link
ENCFF690UHQ ENCFF690UHQ.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 76.3 MB link
ENCFF236OXV ENCFF236OXV.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 78.9 MB link
ENCFF875NQR ENCFF875NQR.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 86.7 MB link
ENCFF914GKJ ENCFF914GKJ.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 78.6 MB link
ENCFF936NUD ENCFF936NUD.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 85.7 MB link
ENCFF318FQC ENCFF318FQC.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V29 plus strand signal of all reads GRCh38 86.7 MB link
ENCFF472BSS ENCFF472BSS.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V29 plus strand signal of all reads GRCh38 85.8 MB link
ENCFF108JNY ENCFF108JNY.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 85.7 MB link
ENCFF217RGZ ENCFF217RGZ.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 80.0 MB link
ENCFF392YXI ENCFF392YXI.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 85.7 MB link
ENCFF416VLQ ENCFF416VLQ.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 77.9 MB link
ENCFF704XUG ENCFF704XUG.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 76.6 MB link
ENCFF822KOL ENCFF822KOL.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 79.9 MB link
ENCFF432LNX ENCFF432LNX.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 79.2 MB link
ENCFF468PNY ENCFF468PNY.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 74.2 MB link
ENCFF488QVJ ENCFF488QVJ.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 74.7 MB link
ENCFF568PCO ENCFF568PCO.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 78.8 MB link
ENCFF373FPM ENCFF373FPM.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 plus strand signal of unique reads GRCh38 79.3 MB link
ENCFF423DIO ENCFF423DIO.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 plus strand signal of unique reads GRCh38 78.8 MB link
ENCFF013MHU ENCFF013MHU.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 72.8 MB link
ENCFF141NZZ ENCFF141NZZ.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 75.1 MB link
ENCFF237RTW ENCFF237RTW.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 72.9 MB link
ENCFF400YQS ENCFF400YQS.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 79.3 MB link
ENCFF586QIW ENCFF586QIW.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 78.8 MB link
ENCFF619MXH ENCFF619MXH.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 74.7 MB link
ENCFF011SMR ENCFF011SMR.fastq fastq (reads) reads 2.9 GB link
ENCFF317GTG ENCFF317GTG.fastq fastq (reads) reads 2.8 GB link
ENCFF438PVX ENCFF438PVX.fastq fastq (reads) reads 2.8 GB link
ENCFF454SOJ ENCFF454SOJ.fastq fastq (reads) reads 2.7 GB link
ENCFF243JXJ ENCFF243JXJ.tar tar (differential splicing quantifications); assembly: hg19; genome annotation: V19 differential splicing quantifications hg19 4.2 MB link
ENCFF549QFR ENCFF549QFR.tar tar (differential splicing quantifications); assembly: hg19; genome annotation: V19 differential splicing quantifications hg19 3.4 MB link
ENCFF835DBH ENCFF835DBH.tar tar (differential splicing quantifications); assembly: hg19; genome annotation: V19 differential splicing quantifications hg19 16.1 MB link
ENCFF079YBM ENCFF079YBM.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 1.8 MB link
ENCFF329LWA ENCFF329LWA.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 1.9 MB link
ENCFF551LBD ENCFF551LBD.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 5.5 MB link
ENCFF684MBB ENCFF684MBB.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 3.0 MB link
ENCFF899WWJ ENCFF899WWJ.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 4.3 MB link
ENCFF030GID ENCFF030GID.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V24 gene quantifications GRCh38 9.4 MB link
ENCFF363UJX ENCFF363UJX.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V24 gene quantifications GRCh38 9.4 MB link
ENCFF350KCP ENCFF350KCP.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V29 gene quantifications GRCh38 10.4 MB link
ENCFF401PDR ENCFF401PDR.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V29 gene quantifications GRCh38 10.4 MB link
ENCFF194ZCD ENCFF194ZCD.tsv tsv (gene quantifications); assembly: hg19; genome annotation: V19 gene quantifications hg19 9.1 MB link
ENCFF863NBZ ENCFF863NBZ.tsv tsv (gene quantifications); assembly: hg19; genome annotation: V19 gene quantifications hg19 9.1 MB link
ENCFF061USF ENCFF061USF.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V24 transcript quantifications GRCh38 25.3 MB link
ENCFF492KDC ENCFF492KDC.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V24 transcript quantifications GRCh38 25.3 MB link
ENCFF261WJS ENCFF261WJS.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 29.8 MB link
ENCFF678QVV ENCFF678QVV.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 27.3 MB link
ENCFF735XHK ENCFF735XHK.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 27.3 MB link
ENCFF804PWT ENCFF804PWT.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 29.8 MB link
ENCFF694IHF ENCFF694IHF.tsv tsv (transcript quantifications); assembly: hg19; genome annotation: V19 transcript quantifications hg19 24.9 MB link
ENCFF765YSL ENCFF765YSL.tsv tsv (transcript quantifications); assembly: hg19; genome annotation: V19 transcript quantifications hg19 24.9 MB link