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ENCSR278CHI

ENCSR ENCODE
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RNA-seq on HepG2 cells treated with an shRNA knockdown against SSB. (SSB_BGHLV37)

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

Summary

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

Overall Design

RNA-seq on HepG2 cells treated with an shRNA knockdown against SSB. (SSB_BGHLV37)

Analysis

View Data Processing
Analysis page is available for ENCSR278CHI.

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: 114.2 GB
Assay: shRNA RNA-seq
Target: SSB
Biosample: Homo sapiens HepG2 expressing RNAi targeting H. sapiens SSB
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
ENCFF128NUZ ENCFF128NUZ.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 3.9 GB link
ENCFF286XRM ENCFF286XRM.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 4.5 GB link
ENCFF512ELZ ENCFF512ELZ.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 5.6 GB link
ENCFF695SSC ENCFF695SSC.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 4.8 GB link
ENCFF240JNV ENCFF240JNV.bam bam (alignments); assembly: GRCh38; genome annotation: V29 alignments GRCh38 5.6 GB link
ENCFF509ITM ENCFF509ITM.bam bam (alignments); assembly: GRCh38; genome annotation: V29 alignments GRCh38 4.8 GB link
ENCFF105XIV ENCFF105XIV.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 4.7 GB link
ENCFF166COZ ENCFF166COZ.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 4.2 GB link
ENCFF196ESE ENCFF196ESE.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 3.9 GB link
ENCFF647DVY ENCFF647DVY.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 5.2 GB link
ENCFF890MYC ENCFF890MYC.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 4.2 GB link
ENCFF962AAW ENCFF962AAW.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 3.9 GB link
ENCFF611YKH ENCFF611YKH.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V24 transcriptome alignments GRCh38 7.1 GB link
ENCFF903XBM ENCFF903XBM.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V24 transcriptome alignments GRCh38 6.6 GB link
ENCFF031GVF ENCFF031GVF.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V29 transcriptome alignments GRCh38 7.5 GB link
ENCFF036NSH ENCFF036NSH.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V29 transcriptome alignments GRCh38 8.0 GB link
ENCFF440CZZ ENCFF440CZZ.bam bam (transcriptome alignments); assembly: hg19; genome annotation: V19 transcriptome alignments hg19 6.5 GB link
ENCFF641MKX ENCFF641MKX.bam bam (transcriptome alignments); assembly: hg19; genome annotation: V19 transcriptome alignments hg19 6.9 GB link
ENCFF534YWH ENCFF534YWH.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 106.7 MB link
ENCFF652HUI ENCFF652HUI.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 96.4 MB link
ENCFF853LMU ENCFF853LMU.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 97.2 MB link
ENCFF957QHI ENCFF957QHI.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 87.7 MB link
ENCFF319UQQ ENCFF319UQQ.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V29 minus strand signal of all reads GRCh38 106.7 MB link
ENCFF936XWE ENCFF936XWE.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V29 minus strand signal of all reads GRCh38 96.5 MB link
ENCFF222OMX ENCFF222OMX.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 95.7 MB link
ENCFF440MJP ENCFF440MJP.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 90.0 MB link
ENCFF451YLC ENCFF451YLC.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 105.9 MB link
ENCFF746WFT ENCFF746WFT.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 94.2 MB link
ENCFF782GFD ENCFF782GFD.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 99.0 MB link
ENCFF823ORR ENCFF823ORR.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 86.5 MB link
ENCFF350LVR ENCFF350LVR.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 87.0 MB link
ENCFF557ZAG ENCFF557ZAG.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 95.7 MB link
ENCFF558QDY ENCFF558QDY.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 91.1 MB link
ENCFF863YNJ ENCFF863YNJ.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 82.0 MB link
ENCFF407IEX ENCFF407IEX.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 minus strand signal of unique reads GRCh38 95.8 MB link
ENCFF761QDZ ENCFF761QDZ.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 minus strand signal of unique reads GRCh38 87.0 MB link
ENCFF098QOO ENCFF098QOO.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 95.8 MB link
ENCFF354PQL ENCFF354PQL.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 87.9 MB link
ENCFF373GNI ENCFF373GNI.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 80.0 MB link
ENCFF493NEN ENCFF493NEN.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 91.0 MB link
ENCFF541ISO ENCFF541ISO.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 86.0 MB link
ENCFF812WHP ENCFF812WHP.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 83.4 MB link
ENCFF174DML ENCFF174DML.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 98.1 MB link
ENCFF600HYE ENCFF600HYE.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 108.5 MB link
ENCFF733JNG ENCFF733JNG.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 99.0 MB link
ENCFF926QHZ ENCFF926QHZ.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 89.2 MB link
ENCFF323NLP ENCFF323NLP.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V29 plus strand signal of all reads GRCh38 98.1 MB link
ENCFF916MSU ENCFF916MSU.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V29 plus strand signal of all reads GRCh38 108.5 MB link
ENCFF034DBK ENCFF034DBK.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 107.4 MB link
ENCFF060APC ENCFF060APC.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 100.9 MB link
ENCFF328UCC ENCFF328UCC.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 88.1 MB link
ENCFF373EQT ENCFF373EQT.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 97.0 MB link
ENCFF456IPV ENCFF456IPV.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 91.7 MB link
ENCFF809LEA ENCFF809LEA.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 95.9 MB link
ENCFF030BCH ENCFF030BCH.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 89.3 MB link
ENCFF469FHI ENCFF469FHI.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 84.0 MB link
ENCFF612OUL ENCFF612OUL.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 93.4 MB link
ENCFF803MPG ENCFF803MPG.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 98.2 MB link
ENCFF483SGN ENCFF483SGN.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 plus strand signal of unique reads GRCh38 98.2 MB link
ENCFF711WVQ ENCFF711WVQ.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 plus strand signal of unique reads GRCh38 89.3 MB link
ENCFF027QWX ENCFF027QWX.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 93.5 MB link
ENCFF277KWA ENCFF277KWA.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 85.6 MB link
ENCFF518BQX ENCFF518BQX.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 90.3 MB link
ENCFF705NPV ENCFF705NPV.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 82.3 MB link
ENCFF848SSX ENCFF848SSX.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 98.3 MB link
ENCFF892XZI ENCFF892XZI.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 88.3 MB link
ENCFF327LHH ENCFF327LHH.fastq fastq (reads) reads 2.8 GB link
ENCFF329XPA ENCFF329XPA.fastq fastq (reads) reads 2.7 GB link
ENCFF578DXQ ENCFF578DXQ.fastq fastq (reads) reads 3.0 GB link
ENCFF628SKZ ENCFF628SKZ.fastq fastq (reads) reads 3.0 GB link
ENCFF586GYR ENCFF586GYR.tar tar (differential splicing quantifications); assembly: hg19; genome annotation: V19 differential splicing quantifications hg19 18.2 MB link
ENCFF641PHF ENCFF641PHF.tar tar (differential splicing quantifications); assembly: hg19; genome annotation: V19 differential splicing quantifications hg19 4.1 MB link
ENCFF643KMA ENCFF643KMA.tar tar (differential splicing quantifications); assembly: hg19; genome annotation: V19 differential splicing quantifications hg19 5.3 MB link
ENCFF135RYL ENCFF135RYL.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 5.5 MB link
ENCFF492AKC ENCFF492AKC.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 2.0 MB link
ENCFF708FDR ENCFF708FDR.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 1.8 MB link
ENCFF795MRZ ENCFF795MRZ.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 2.7 MB link
ENCFF982WPV ENCFF982WPV.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 4.5 MB link
ENCFF657REP ENCFF657REP.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V24 gene quantifications GRCh38 9.4 MB link
ENCFF819RUU ENCFF819RUU.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V24 gene quantifications GRCh38 9.5 MB link
ENCFF322XEV ENCFF322XEV.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V29 gene quantifications GRCh38 10.4 MB link
ENCFF837VFH ENCFF837VFH.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V29 gene quantifications GRCh38 10.4 MB link
ENCFF136CHI ENCFF136CHI.tsv tsv (gene quantifications); assembly: hg19; genome annotation: V19 gene quantifications hg19 9.1 MB link
ENCFF265WBI ENCFF265WBI.tsv tsv (gene quantifications); assembly: hg19; genome annotation: V19 gene quantifications hg19 9.1 MB link
ENCFF084EGD ENCFF084EGD.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V24 transcript quantifications GRCh38 25.3 MB link
ENCFF393CGW ENCFF393CGW.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V24 transcript quantifications GRCh38 25.3 MB link
ENCFF149MGL ENCFF149MGL.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 29.8 MB link
ENCFF732LHR ENCFF732LHR.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 27.4 MB link
ENCFF926LUP ENCFF926LUP.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 29.8 MB link
ENCFF931NCM ENCFF931NCM.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 27.4 MB link
ENCFF290DBW ENCFF290DBW.tsv tsv (transcript quantifications); assembly: hg19; genome annotation: V19 transcript quantifications hg19 24.9 MB link
ENCFF761PCZ ENCFF761PCZ.tsv tsv (transcript quantifications); assembly: hg19; genome annotation: V19 transcript quantifications hg19 24.9 MB link