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ENCSR269ZAO

ENCSR ENCODE
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RNA-seq on HepG2 cells treated with an shRNA knockdown against UTP18. (UTP18_BGHLV33)

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

Summary

shRNA RNA-seq of UTP18 in Homo sapiens HepG2 expressing RNAi targeting H. sapiens UTP18

Overall Design

RNA-seq on HepG2 cells treated with an shRNA knockdown against UTP18. (UTP18_BGHLV33)

Analysis

View Data Processing
Analysis page is available for ENCSR269ZAO.

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: 117.9 GB
Assay: shRNA RNA-seq
Target: UTP18
Biosample: Homo sapiens HepG2 expressing RNAi targeting H. sapiens UTP18
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
ENCFF103VZY ENCFF103VZY.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 5.7 GB link
ENCFF312XOU ENCFF312XOU.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 4.7 GB link
ENCFF452EMG ENCFF452EMG.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 5.6 GB link
ENCFF640ECA ENCFF640ECA.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 4.6 GB link
ENCFF142CMC ENCFF142CMC.bam bam (alignments); assembly: GRCh38; genome annotation: V29 alignments GRCh38 5.7 GB link
ENCFF468UQW ENCFF468UQW.bam bam (alignments); assembly: GRCh38; genome annotation: V29 alignments GRCh38 5.6 GB link
ENCFF119XOV ENCFF119XOV.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 4.5 GB link
ENCFF202TGW ENCFF202TGW.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 5.4 GB link
ENCFF219OWH ENCFF219OWH.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 4.6 GB link
ENCFF452ZCF ENCFF452ZCF.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 4.6 GB link
ENCFF576LMK ENCFF576LMK.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 4.5 GB link
ENCFF977IXL ENCFF977IXL.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 5.5 GB link
ENCFF066LMO ENCFF066LMO.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V24 transcriptome alignments GRCh38 6.3 GB link
ENCFF934HHN ENCFF934HHN.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V24 transcriptome alignments GRCh38 6.6 GB link
ENCFF074AJG ENCFF074AJG.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V29 transcriptome alignments GRCh38 7.1 GB link
ENCFF542XAO ENCFF542XAO.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V29 transcriptome alignments GRCh38 7.5 GB link
ENCFF326QFF ENCFF326QFF.bam bam (transcriptome alignments); assembly: hg19; genome annotation: V19 transcriptome alignments hg19 6.6 GB link
ENCFF933ROZ ENCFF933ROZ.bam bam (transcriptome alignments); assembly: hg19; genome annotation: V19 transcriptome alignments hg19 6.3 GB link
ENCFF025RNG ENCFF025RNG.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 81.2 MB link
ENCFF047OTV ENCFF047OTV.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 93.5 MB link
ENCFF220TTF ENCFF220TTF.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 82.6 MB link
ENCFF681QBU ENCFF681QBU.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 94.2 MB link
ENCFF548OTW ENCFF548OTW.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V29 minus strand signal of all reads GRCh38 93.5 MB link
ENCFF577BJT ENCFF577BJT.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V29 minus strand signal of all reads GRCh38 94.2 MB link
ENCFF026DSE ENCFF026DSE.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 81.0 MB link
ENCFF053ZEU ENCFF053ZEU.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 85.0 MB link
ENCFF371XWY ENCFF371XWY.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 93.9 MB link
ENCFF442YUZ ENCFF442YUZ.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 82.8 MB link
ENCFF501ZSN ENCFF501ZSN.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 92.0 MB link
ENCFF827AMR ENCFF827AMR.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 79.2 MB link
ENCFF092KPR ENCFF092KPR.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 83.4 MB link
ENCFF135HVO ENCFF135HVO.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 77.9 MB link
ENCFF171FNO ENCFF171FNO.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 84.6 MB link
ENCFF273XDC ENCFF273XDC.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 76.8 MB link
ENCFF385IHE ENCFF385IHE.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 minus strand signal of unique reads GRCh38 84.6 MB link
ENCFF768VZA ENCFF768VZA.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 minus strand signal of unique reads GRCh38 83.4 MB link
ENCFF222QAI ENCFF222QAI.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 77.9 MB link
ENCFF275UEU ENCFF275UEU.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 75.4 MB link
ENCFF411XCV ENCFF411XCV.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 83.4 MB link
ENCFF735PWU ENCFF735PWU.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 83.4 MB link
ENCFF831WGP ENCFF831WGP.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 76.8 MB link
ENCFF854OTA ENCFF854OTA.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 73.2 MB link
ENCFF206DWC ENCFF206DWC.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 82.7 MB link
ENCFF513YMD ENCFF513YMD.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 95.2 MB link
ENCFF719BNL ENCFF719BNL.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 96.0 MB link
ENCFF808NQJ ENCFF808NQJ.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 84.2 MB link
ENCFF434GUP ENCFF434GUP.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V29 plus strand signal of all reads GRCh38 96.0 MB link
ENCFF952TUA ENCFF952TUA.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V29 plus strand signal of all reads GRCh38 95.2 MB link
ENCFF250FFD ENCFF250FFD.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 95.5 MB link
ENCFF382EMX ENCFF382EMX.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 86.8 MB link
ENCFF586ZNH ENCFF586ZNH.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 84.4 MB link
ENCFF603PDU ENCFF603PDU.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 81.0 MB link
ENCFF689OMV ENCFF689OMV.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 83.0 MB link
ENCFF955WAO ENCFF955WAO.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 93.5 MB link
ENCFF330KIF ENCFF330KIF.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 86.9 MB link
ENCFF352GHD ENCFF352GHD.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 78.7 MB link
ENCFF429VRZ ENCFF429VRZ.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 79.9 MB link
ENCFF491LSG ENCFF491LSG.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 85.6 MB link
ENCFF158ATY ENCFF158ATY.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 plus strand signal of unique reads GRCh38 86.9 MB link
ENCFF946BAP ENCFF946BAP.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 plus strand signal of unique reads GRCh38 85.6 MB link
ENCFF216IHO ENCFF216IHO.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 85.7 MB link
ENCFF257FKO ENCFF257FKO.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 77.8 MB link
ENCFF384KOK ENCFF384KOK.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 75.4 MB link
ENCFF452ICY ENCFF452ICY.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 78.9 MB link
ENCFF520SJB ENCFF520SJB.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 85.7 MB link
ENCFF549LTF ENCFF549LTF.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 80.1 MB link
ENCFF444BKK ENCFF444BKK.fastq fastq (reads) reads 3.0 GB link
ENCFF605VXW ENCFF605VXW.fastq fastq (reads) reads 3.1 GB link
ENCFF913ZEI ENCFF913ZEI.fastq fastq (reads) reads 3.1 GB link
ENCFF924EZD ENCFF924EZD.fastq fastq (reads) reads 3.0 GB link
ENCFF043NQT ENCFF043NQT.tar tar (differential splicing quantifications); assembly: hg19; genome annotation: V19 differential splicing quantifications hg19 4.3 MB link
ENCFF331CEB ENCFF331CEB.tar tar (differential splicing quantifications); assembly: hg19; genome annotation: V19 differential splicing quantifications hg19 16.9 MB link
ENCFF601PIY ENCFF601PIY.tar tar (differential splicing quantifications); assembly: hg19; genome annotation: V19 differential splicing quantifications hg19 3.5 MB link
ENCFF155YES ENCFF155YES.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 2.0 MB link
ENCFF830LLT ENCFF830LLT.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 1.6 MB link
ENCFF848WYS ENCFF848WYS.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 5.6 MB link
ENCFF860PHK ENCFF860PHK.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 4.3 MB link
ENCFF976JTC ENCFF976JTC.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 2.9 MB link
ENCFF012QOZ ENCFF012QOZ.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V24 gene quantifications GRCh38 9.5 MB link
ENCFF769BSG ENCFF769BSG.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V24 gene quantifications GRCh38 9.5 MB link
ENCFF075GYT ENCFF075GYT.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V29 gene quantifications GRCh38 10.4 MB link
ENCFF225RUG ENCFF225RUG.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V29 gene quantifications GRCh38 10.4 MB link
ENCFF102XVG ENCFF102XVG.tsv tsv (gene quantifications); assembly: hg19; genome annotation: V19 gene quantifications hg19 9.1 MB link
ENCFF633YPB ENCFF633YPB.tsv tsv (gene quantifications); assembly: hg19; genome annotation: V19 gene quantifications hg19 9.1 MB link
ENCFF771AWU ENCFF771AWU.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V24 transcript quantifications GRCh38 25.3 MB link
ENCFF783IAP ENCFF783IAP.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V24 transcript quantifications GRCh38 25.3 MB link
ENCFF061QWO ENCFF061QWO.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 29.8 MB link
ENCFF209NHJ ENCFF209NHJ.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 27.3 MB link
ENCFF833GKU ENCFF833GKU.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 27.4 MB link
ENCFF977UDP ENCFF977UDP.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 29.8 MB link
ENCFF302THZ ENCFF302THZ.tsv tsv (transcript quantifications); assembly: hg19; genome annotation: V19 transcript quantifications hg19 24.9 MB link
ENCFF790GEI ENCFF790GEI.tsv tsv (transcript quantifications); assembly: hg19; genome annotation: V19 transcript quantifications hg19 24.9 MB link