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ENCSR837QDN

ENCSR ENCODE
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RNA-seq on HepG2 cells treated with an shRNA knockdown against SUGP2. (SUGP2_BGHLV27)

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

Summary

shRNA RNA-seq of SUGP2 in Homo sapiens HepG2 expressing RNAi targeting H. sapiens SUGP2

Overall Design

RNA-seq on HepG2 cells treated with an shRNA knockdown against SUGP2. (SUGP2_BGHLV27)

Analysis

View Data Processing
Analysis page is available for ENCSR837QDN.

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: 132.2 GB
Assay: shRNA RNA-seq
Target: SUGP2
Biosample: Homo sapiens HepG2 expressing RNAi targeting H. sapiens SUGP2
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
ENCFF300GUU ENCFF300GUU.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 6.2 GB link
ENCFF345GOM ENCFF345GOM.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 4.7 GB link
ENCFF838ARB ENCFF838ARB.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 5.9 GB link
ENCFF989TRB ENCFF989TRB.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 5.1 GB link
ENCFF277XYJ ENCFF277XYJ.bam bam (alignments); assembly: GRCh38; genome annotation: V29 alignments GRCh38 6.2 GB link
ENCFF960IJT ENCFF960IJT.bam bam (alignments); assembly: GRCh38; genome annotation: V29 alignments GRCh38 5.9 GB link
ENCFF267PPI ENCFF267PPI.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 4.5 GB link
ENCFF375BBI ENCFF375BBI.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 4.9 GB link
ENCFF384IPG ENCFF384IPG.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 4.9 GB link
ENCFF434QDG ENCFF434QDG.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 5.5 GB link
ENCFF622PET ENCFF622PET.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 6.0 GB link
ENCFF716BPQ ENCFF716BPQ.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 4.5 GB link
ENCFF579MJO ENCFF579MJO.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V24 transcriptome alignments GRCh38 8.2 GB link
ENCFF588HUI ENCFF588HUI.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V24 transcriptome alignments GRCh38 7.7 GB link
ENCFF595EBE ENCFF595EBE.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V29 transcriptome alignments GRCh38 9.3 GB link
ENCFF941VXO ENCFF941VXO.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V29 transcriptome alignments GRCh38 8.7 GB link
ENCFF285KVL ENCFF285KVL.bam bam (transcriptome alignments); assembly: hg19; genome annotation: V19 transcriptome alignments hg19 8.2 GB link
ENCFF314WKY ENCFF314WKY.bam bam (transcriptome alignments); assembly: hg19; genome annotation: V19 transcriptome alignments hg19 7.6 GB link
ENCFF184TQK ENCFF184TQK.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 92.2 MB link
ENCFF541CIR ENCFF541CIR.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 99.1 MB link
ENCFF652QRB ENCFF652QRB.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 101.9 MB link
ENCFF971KHQ ENCFF971KHQ.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 91.0 MB link
ENCFF276ISI ENCFF276ISI.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V29 minus strand signal of all reads GRCh38 99.1 MB link
ENCFF461LRL ENCFF461LRL.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V29 minus strand signal of all reads GRCh38 101.9 MB link
ENCFF040YLG ENCFF040YLG.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 98.9 MB link
ENCFF461TSS ENCFF461TSS.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 88.7 MB link
ENCFF681JJH ENCFF681JJH.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 92.7 MB link
ENCFF837JIY ENCFF837JIY.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 94.0 MB link
ENCFF895JAB ENCFF895JAB.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 99.3 MB link
ENCFF965FRA ENCFF965FRA.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 89.1 MB link
ENCFF637PSF ENCFF637PSF.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 85.1 MB link
ENCFF919UYI ENCFF919UYI.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 86.2 MB link
ENCFF947TAD ENCFF947TAD.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 89.3 MB link
ENCFF963FTP ENCFF963FTP.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 90.8 MB link
ENCFF204LGR ENCFF204LGR.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 minus strand signal of unique reads GRCh38 89.3 MB link
ENCFF269HSI ENCFF269HSI.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 minus strand signal of unique reads GRCh38 90.3 MB link
ENCFF006XSF ENCFF006XSF.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 89.9 MB link
ENCFF122JCE ENCFF122JCE.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 82.6 MB link
ENCFF241ZSP ENCFF241ZSP.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 88.8 MB link
ENCFF320IIZ ENCFF320IIZ.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 85.7 MB link
ENCFF797PKX ENCFF797PKX.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 82.0 MB link
ENCFF984YAD ENCFF984YAD.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 86.7 MB link
ENCFF499CMK ENCFF499CMK.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 91.8 MB link
ENCFF499VBE ENCFF499VBE.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 102.6 MB link
ENCFF701CFH ENCFF701CFH.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 99.9 MB link
ENCFF823WOW ENCFF823WOW.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 92.9 MB link
ENCFF340LVL ENCFF340LVL.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V29 plus strand signal of all reads GRCh38 102.6 MB link
ENCFF628CPY ENCFF628CPY.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V29 plus strand signal of all reads GRCh38 99.8 MB link
ENCFF700BQX ENCFF700BQX.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 99.5 MB link
ENCFF761PTJ ENCFF761PTJ.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 94.9 MB link
ENCFF767RDF ENCFF767RDF.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 93.6 MB link
ENCFF836UAW ENCFF836UAW.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 100.0 MB link
ENCFF860TKV ENCFF860TKV.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 90.1 MB link
ENCFF874FDT ENCFF874FDT.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 89.6 MB link
ENCFF331DPA ENCFF331DPA.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 87.5 MB link
ENCFF418JYE ENCFF418JYE.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 92.2 MB link
ENCFF887FLG ENCFF887FLG.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 90.8 MB link
ENCFF945BDD ENCFF945BDD.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 86.4 MB link
ENCFF053KVX ENCFF053KVX.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 plus strand signal of unique reads GRCh38 90.8 MB link
ENCFF385NCP ENCFF385NCP.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 plus strand signal of unique reads GRCh38 91.7 MB link
ENCFF098KES ENCFF098KES.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 87.2 MB link
ENCFF169GPT ENCFF169GPT.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 90.3 MB link
ENCFF544QWK ENCFF544QWK.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 88.2 MB link
ENCFF548AYH ENCFF548AYH.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 83.5 MB link
ENCFF706WEI ENCFF706WEI.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 84.3 MB link
ENCFF948ZDX ENCFF948ZDX.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 91.4 MB link
ENCFF167MYT ENCFF167MYT.fastq fastq (reads) reads 3.6 GB link
ENCFF220WUH ENCFF220WUH.fastq fastq (reads) reads 3.5 GB link
ENCFF259LFX ENCFF259LFX.fastq fastq (reads) reads 3.3 GB link
ENCFF624OJV ENCFF624OJV.fastq fastq (reads) reads 3.3 GB link
ENCFF172APM ENCFF172APM.tar tar (differential splicing quantifications); assembly: hg19; genome annotation: V19 differential splicing quantifications hg19 3.5 MB link
ENCFF330WPX ENCFF330WPX.tar tar (differential splicing quantifications); assembly: hg19; genome annotation: V19 differential splicing quantifications hg19 16.5 MB link
ENCFF651MFV ENCFF651MFV.tar tar (differential splicing quantifications); assembly: hg19; genome annotation: V19 differential splicing quantifications hg19 4.2 MB link
ENCFF026BVU ENCFF026BVU.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 1.8 MB link
ENCFF083BZN ENCFF083BZN.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 4.3 MB link
ENCFF294YPZ ENCFF294YPZ.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 2.6 MB link
ENCFF725FGD ENCFF725FGD.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 5.6 MB link
ENCFF841FHK ENCFF841FHK.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 1.9 MB link
ENCFF380RYA ENCFF380RYA.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V24 gene quantifications GRCh38 9.5 MB link
ENCFF952NFS ENCFF952NFS.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V24 gene quantifications GRCh38 9.5 MB link
ENCFF444ATM ENCFF444ATM.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V29 gene quantifications GRCh38 10.4 MB link
ENCFF494HNY ENCFF494HNY.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V29 gene quantifications GRCh38 10.4 MB link
ENCFF526NTI ENCFF526NTI.tsv tsv (gene quantifications); assembly: hg19; genome annotation: V19 gene quantifications hg19 9.1 MB link
ENCFF806ARA ENCFF806ARA.tsv tsv (gene quantifications); assembly: hg19; genome annotation: V19 gene quantifications hg19 9.1 MB link
ENCFF429TBP ENCFF429TBP.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V24 transcript quantifications GRCh38 25.4 MB link
ENCFF662VHV ENCFF662VHV.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V24 transcript quantifications GRCh38 25.4 MB link
ENCFF275DYN ENCFF275DYN.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 29.9 MB link
ENCFF606LKK ENCFF606LKK.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 27.4 MB link
ENCFF669AAJ ENCFF669AAJ.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 29.9 MB link
ENCFF950SHP ENCFF950SHP.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 27.4 MB link
ENCFF445UOB ENCFF445UOB.tsv tsv (transcript quantifications); assembly: hg19; genome annotation: V19 transcript quantifications hg19 25.0 MB link
ENCFF847SGH ENCFF847SGH.tsv tsv (transcript quantifications); assembly: hg19; genome annotation: V19 transcript quantifications hg19 25.0 MB link