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ENCSR706SXN

ENCSR ENCODE
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shRNA knockdown against RPL23A in HepG2 cells followed by RNA-seq. (RPL23A_BGHLV18)

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

Summary

shRNA RNA-seq of RPL23A in Homo sapiens HepG2 expressing RNAi targeting H. sapiens RPL23A

Overall Design

shRNA knockdown against RPL23A in HepG2 cells followed by RNA-seq. (RPL23A_BGHLV18)

Analysis

View Data Processing
Analysis page is available for ENCSR706SXN.

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: 101.6 GB
Assay: shRNA RNA-seq
Target: RPL23A
Biosample: Homo sapiens HepG2 expressing RNAi targeting H. sapiens RPL23A
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
ENCFF008LKR ENCFF008LKR.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 6.1 GB link
ENCFF031CNE ENCFF031CNE.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 3.3 GB link
ENCFF131YVK ENCFF131YVK.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 3.9 GB link
ENCFF478RJR ENCFF478RJR.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 4.9 GB link
ENCFF112LKY ENCFF112LKY.bam bam (alignments); assembly: GRCh38; genome annotation: V29 alignments GRCh38 6.1 GB link
ENCFF605KYS ENCFF605KYS.bam bam (alignments); assembly: GRCh38; genome annotation: V29 alignments GRCh38 3.9 GB link
ENCFF059YGS ENCFF059YGS.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 5.1 GB link
ENCFF321SLT ENCFF321SLT.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 3.2 GB link
ENCFF783ONX ENCFF783ONX.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 4.3 GB link
ENCFF860CUV ENCFF860CUV.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 4.3 GB link
ENCFF916TOV ENCFF916TOV.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 3.8 GB link
ENCFF958DQA ENCFF958DQA.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 3.2 GB link
ENCFF341ZWA ENCFF341ZWA.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V24 transcriptome alignments GRCh38 6.5 GB link
ENCFF539ROA ENCFF539ROA.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V24 transcriptome alignments GRCh38 4.9 GB link
ENCFF285ZXW ENCFF285ZXW.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V29 transcriptome alignments GRCh38 7.3 GB link
ENCFF479JPH ENCFF479JPH.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V29 transcriptome alignments GRCh38 5.5 GB link
ENCFF813HGN ENCFF813HGN.bam bam (transcriptome alignments); assembly: hg19; genome annotation: V19 transcriptome alignments hg19 4.9 GB link
ENCFF849TYD ENCFF849TYD.bam bam (transcriptome alignments); assembly: hg19; genome annotation: V19 transcriptome alignments hg19 6.5 GB link
ENCFF097FFJ ENCFF097FFJ.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 79.9 MB link
ENCFF454FOK ENCFF454FOK.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 72.3 MB link
ENCFF690SAZ ENCFF690SAZ.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 65.5 MB link
ENCFF953DZL ENCFF953DZL.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 87.6 MB link
ENCFF305VZH ENCFF305VZH.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V29 minus strand signal of all reads GRCh38 87.6 MB link
ENCFF818YDS ENCFF818YDS.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V29 minus strand signal of all reads GRCh38 72.3 MB link
ENCFF187AED ENCFF187AED.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 78.1 MB link
ENCFF211EWC ENCFF211EWC.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 71.7 MB link
ENCFF565NCD ENCFF565NCD.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 66.4 MB link
ENCFF713GYR ENCFF713GYR.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 63.5 MB link
ENCFF930ORR ENCFF930ORR.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 86.7 MB link
ENCFF955UAY ENCFF955UAY.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 81.1 MB link
ENCFF398OEK ENCFF398OEK.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 60.8 MB link
ENCFF788FOV ENCFF788FOV.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 75.0 MB link
ENCFF821LNZ ENCFF821LNZ.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 78.3 MB link
ENCFF884GTD ENCFF884GTD.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 65.0 MB link
ENCFF535BCY ENCFF535BCY.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 minus strand signal of unique reads GRCh38 65.0 MB link
ENCFF545VIE ENCFF545VIE.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 minus strand signal of unique reads GRCh38 78.2 MB link
ENCFF233VTN ENCFF233VTN.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 64.6 MB link
ENCFF395LTQ ENCFF395LTQ.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 72.7 MB link
ENCFF685IAT ENCFF685IAT.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 59.1 MB link
ENCFF744CMI ENCFF744CMI.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 78.2 MB link
ENCFF908CMF ENCFF908CMF.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 61.8 MB link
ENCFF962ATJ ENCFF962ATJ.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 75.4 MB link
ENCFF229GAB ENCFF229GAB.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 66.7 MB link
ENCFF359MRN ENCFF359MRN.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 89.1 MB link
ENCFF479PFI ENCFF479PFI.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 81.3 MB link
ENCFF617MUC ENCFF617MUC.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 73.5 MB link
ENCFF003MMZ ENCFF003MMZ.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V29 plus strand signal of all reads GRCh38 73.5 MB link
ENCFF408YHV ENCFF408YHV.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V29 plus strand signal of all reads GRCh38 89.2 MB link
ENCFF158OWV ENCFF158OWV.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 67.7 MB link
ENCFF201PMF ENCFF201PMF.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 79.8 MB link
ENCFF254UMV ENCFF254UMV.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 64.8 MB link
ENCFF699WWV ENCFF699WWV.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 82.7 MB link
ENCFF944KYU ENCFF944KYU.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 88.1 MB link
ENCFF978CWE ENCFF978CWE.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 72.8 MB link
ENCFF006SJD ENCFF006SJD.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 80.4 MB link
ENCFF219YZF ENCFF219YZF.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 76.8 MB link
ENCFF369QBK ENCFF369QBK.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 66.7 MB link
ENCFF689NJW ENCFF689NJW.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 62.3 MB link
ENCFF251REA ENCFF251REA.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 plus strand signal of unique reads GRCh38 66.6 MB link
ENCFF585POB ENCFF585POB.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 plus strand signal of unique reads GRCh38 80.3 MB link
ENCFF041XDE ENCFF041XDE.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 77.5 MB link
ENCFF152ZNP ENCFF152ZNP.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 80.3 MB link
ENCFF256VVE ENCFF256VVE.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 66.3 MB link
ENCFF259DBM ENCFF259DBM.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 60.9 MB link
ENCFF460FAD ENCFF460FAD.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 74.9 MB link
ENCFF461PDY ENCFF461PDY.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 63.5 MB link
ENCFF315AQR ENCFF315AQR.fastq fastq (reads) reads 2.8 GB link
ENCFF593XTS ENCFF593XTS.fastq fastq (reads) reads 2.1 GB link
ENCFF665BGI ENCFF665BGI.fastq fastq (reads) reads 2.9 GB link
ENCFF985OVL ENCFF985OVL.fastq fastq (reads) reads 2.2 GB link
ENCFF057JNB ENCFF057JNB.tar tar (differential splicing quantifications); assembly: hg19; genome annotation: V19 differential splicing quantifications hg19 15.2 MB link
ENCFF259FFA ENCFF259FFA.tar tar (differential splicing quantifications); assembly: hg19; genome annotation: V19 differential splicing quantifications hg19 3.2 MB link
ENCFF488NTT ENCFF488NTT.tar tar (differential splicing quantifications); assembly: hg19; genome annotation: V19 differential splicing quantifications hg19 3.7 MB link
ENCFF332VZE ENCFF332VZE.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 4.1 MB link
ENCFF366LHA ENCFF366LHA.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 2.0 MB link
ENCFF408NTE ENCFF408NTE.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 5.6 MB link
ENCFF556OBI ENCFF556OBI.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 2.7 MB link
ENCFF744BEA ENCFF744BEA.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 1.8 MB link
ENCFF073DHZ ENCFF073DHZ.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V24 gene quantifications GRCh38 9.5 MB link
ENCFF296TBL ENCFF296TBL.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V24 gene quantifications GRCh38 9.4 MB link
ENCFF031WXP ENCFF031WXP.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V29 gene quantifications GRCh38 10.4 MB link
ENCFF040PQN ENCFF040PQN.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V29 gene quantifications GRCh38 10.4 MB link
ENCFF178VCW ENCFF178VCW.tsv tsv (gene quantifications); assembly: hg19; genome annotation: V19 gene quantifications hg19 9.1 MB link
ENCFF699OJU ENCFF699OJU.tsv tsv (gene quantifications); assembly: hg19; genome annotation: V19 gene quantifications hg19 9.1 MB link
ENCFF241PSP ENCFF241PSP.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V24 transcript quantifications GRCh38 25.3 MB link
ENCFF299PQX ENCFF299PQX.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V24 transcript quantifications GRCh38 25.3 MB link
ENCFF405DSR ENCFF405DSR.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 27.4 MB link
ENCFF410DHZ ENCFF410DHZ.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 29.8 MB link
ENCFF455OKF ENCFF455OKF.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 27.3 MB link
ENCFF687RQT ENCFF687RQT.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 29.8 MB link
ENCFF189OCG ENCFF189OCG.tsv tsv (transcript quantifications); assembly: hg19; genome annotation: V19 transcript quantifications hg19 24.9 MB link
ENCFF733PVX ENCFF733PVX.tsv tsv (transcript quantifications); assembly: hg19; genome annotation: V19 transcript quantifications hg19 24.9 MB link