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ENCSR222SMI

ENCSR ENCODE
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shRNA knockdown against RBM27 in HepG2 cells followed by RNA-seq. (RBM27_BGHLV18)

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

Summary

shRNA RNA-seq of RBM27 in Homo sapiens HepG2 expressing RNAi targeting H. sapiens RBM27

Overall Design

shRNA knockdown against RBM27 in HepG2 cells followed by RNA-seq. (RBM27_BGHLV18)

Analysis

View Data Processing
Analysis page is available for ENCSR222SMI.

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: 126.6 GB
Assay: shRNA RNA-seq
Target: RBM27
Biosample: Homo sapiens HepG2 expressing RNAi targeting H. sapiens RBM27
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
ENCFF006KZA ENCFF006KZA.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 4.0 GB link
ENCFF543EPJ ENCFF543EPJ.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 7.0 GB link
ENCFF725YFX ENCFF725YFX.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 4.8 GB link
ENCFF989HAQ ENCFF989HAQ.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 5.8 GB link
ENCFF405BFY ENCFF405BFY.bam bam (alignments); assembly: GRCh38; genome annotation: V29 alignments GRCh38 7.0 GB link
ENCFF681YPI ENCFF681YPI.bam bam (alignments); assembly: GRCh38; genome annotation: V29 alignments GRCh38 4.8 GB link
ENCFF241FYW ENCFF241FYW.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 6.8 GB link
ENCFF377BGQ ENCFF377BGQ.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 4.0 GB link
ENCFF457JDA ENCFF457JDA.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 5.8 GB link
ENCFF530BTB ENCFF530BTB.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 4.0 GB link
ENCFF541ADT ENCFF541ADT.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 4.7 GB link
ENCFF964OSF ENCFF964OSF.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 5.8 GB link
ENCFF598ZON ENCFF598ZON.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V24 transcriptome alignments GRCh38 8.6 GB link
ENCFF921IIC ENCFF921IIC.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V24 transcriptome alignments GRCh38 5.8 GB link
ENCFF682IYV ENCFF682IYV.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V29 transcriptome alignments GRCh38 6.5 GB link
ENCFF939GGY ENCFF939GGY.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V29 transcriptome alignments GRCh38 9.6 GB link
ENCFF228EPR ENCFF228EPR.bam bam (transcriptome alignments); assembly: hg19; genome annotation: V19 transcriptome alignments hg19 5.8 GB link
ENCFF827OZE ENCFF827OZE.bam bam (transcriptome alignments); assembly: hg19; genome annotation: V19 transcriptome alignments hg19 8.5 GB link
ENCFF152UUK ENCFF152UUK.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 89.8 MB link
ENCFF344DQY ENCFF344DQY.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 109.2 MB link
ENCFF417VJE ENCFF417VJE.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 81.0 MB link
ENCFF586XIW ENCFF586XIW.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 97.9 MB link
ENCFF166VQA ENCFF166VQA.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V29 minus strand signal of all reads GRCh38 89.8 MB link
ENCFF780OZZ ENCFF780OZZ.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V29 minus strand signal of all reads GRCh38 109.2 MB link
ENCFF193OIG ENCFF193OIG.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 108.4 MB link
ENCFF633DJB ENCFF633DJB.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 100.4 MB link
ENCFF735PSO ENCFF735PSO.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 82.3 MB link
ENCFF750JPK ENCFF750JPK.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 89.5 MB link
ENCFF863TYQ ENCFF863TYQ.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 96.8 MB link
ENCFF952IPO ENCFF952IPO.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 77.7 MB link
ENCFF190NSV ENCFF190NSV.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 79.9 MB link
ENCFF232ONU ENCFF232ONU.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 92.1 MB link
ENCFF389EVI ENCFF389EVI.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 76.0 MB link
ENCFF758SGB ENCFF758SGB.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 98.2 MB link
ENCFF356EJT ENCFF356EJT.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 minus strand signal of unique reads GRCh38 97.6 MB link
ENCFF550MOX ENCFF550MOX.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 minus strand signal of unique reads GRCh38 80.0 MB link
ENCFF024FWL ENCFF024FWL.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 76.5 MB link
ENCFF107UXQ ENCFF107UXQ.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 79.9 MB link
ENCFF177KCH ENCFF177KCH.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 97.5 MB link
ENCFF480DSR ENCFF480DSR.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 93.2 MB link
ENCFF792NIO ENCFF792NIO.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 90.0 MB link
ENCFF860COA ENCFF860COA.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 73.4 MB link
ENCFF582LXI ENCFF582LXI.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 111.1 MB link
ENCFF677ELI ENCFF677ELI.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 99.7 MB link
ENCFF773ZAO ENCFF773ZAO.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 91.4 MB link
ENCFF819GEJ ENCFF819GEJ.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 82.5 MB link
ENCFF206ZFI ENCFF206ZFI.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V29 plus strand signal of all reads GRCh38 111.1 MB link
ENCFF556RXO ENCFF556RXO.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V29 plus strand signal of all reads GRCh38 91.4 MB link
ENCFF015ZVH ENCFF015ZVH.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 102.3 MB link
ENCFF096KZX ENCFF096KZX.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 90.9 MB link
ENCFF554FMS ENCFF554FMS.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 84.0 MB link
ENCFF632HEX ENCFF632HEX.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 99.0 MB link
ENCFF868JXH ENCFF868JXH.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 79.4 MB link
ENCFF884IPA ENCFF884IPA.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 110.1 MB link
ENCFF225HNX ENCFF225HNX.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 78.0 MB link
ENCFF545IWB ENCFF545IWB.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 100.7 MB link
ENCFF850XIH ENCFF850XIH.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 82.1 MB link
ENCFF919TDH ENCFF919TDH.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 94.3 MB link
ENCFF253JQB ENCFF253JQB.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 plus strand signal of unique reads GRCh38 100.1 MB link
ENCFF699DXS ENCFF699DXS.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 plus strand signal of unique reads GRCh38 82.2 MB link
ENCFF209LHJ ENCFF209LHJ.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 100.2 MB link
ENCFF359ISM ENCFF359ISM.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 92.7 MB link
ENCFF567UNW ENCFF567UNW.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 82.1 MB link
ENCFF571PHT ENCFF571PHT.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 75.6 MB link
ENCFF700RLT ENCFF700RLT.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 95.7 MB link
ENCFF786UEO ENCFF786UEO.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 78.7 MB link
ENCFF491ZUL ENCFF491ZUL.fastq fastq (reads) reads 2.6 GB link
ENCFF542HCB ENCFF542HCB.fastq fastq (reads) reads 3.7 GB link
ENCFF844NNV ENCFF844NNV.fastq fastq (reads) reads 3.8 GB link
ENCFF902HPG ENCFF902HPG.fastq fastq (reads) reads 2.5 GB link
ENCFF302CBE ENCFF302CBE.tar tar (differential splicing quantifications); assembly: hg19; genome annotation: V19 differential splicing quantifications hg19 3.6 MB link
ENCFF733PFH ENCFF733PFH.tar tar (differential splicing quantifications); assembly: hg19; genome annotation: V19 differential splicing quantifications hg19 4.3 MB link
ENCFF863RJJ ENCFF863RJJ.tar tar (differential splicing quantifications); assembly: hg19; genome annotation: V19 differential splicing quantifications hg19 15.7 MB link
ENCFF668QGC ENCFF668QGC.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 2.0 MB link
ENCFF676BAS ENCFF676BAS.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 4.3 MB link
ENCFF742KDH ENCFF742KDH.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 1.7 MB link
ENCFF784WSC ENCFF784WSC.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 2.9 MB link
ENCFF840SFN ENCFF840SFN.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 5.6 MB link
ENCFF125KIZ ENCFF125KIZ.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V24 gene quantifications GRCh38 9.5 MB link
ENCFF656BZU ENCFF656BZU.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V24 gene quantifications GRCh38 9.4 MB link
ENCFF594ICS ENCFF594ICS.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V29 gene quantifications GRCh38 10.4 MB link
ENCFF853VPB ENCFF853VPB.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V29 gene quantifications GRCh38 10.4 MB link
ENCFF035CDE ENCFF035CDE.tsv tsv (gene quantifications); assembly: hg19; genome annotation: V19 gene quantifications hg19 9.1 MB link
ENCFF963ZAD ENCFF963ZAD.tsv tsv (gene quantifications); assembly: hg19; genome annotation: V19 gene quantifications hg19 9.1 MB link
ENCFF663NGD ENCFF663NGD.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V24 transcript quantifications GRCh38 25.3 MB link
ENCFF850OKG ENCFF850OKG.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V24 transcript quantifications GRCh38 25.3 MB link
ENCFF177RWX ENCFF177RWX.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 29.8 MB link
ENCFF824GAJ ENCFF824GAJ.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 27.4 MB link
ENCFF951AAF ENCFF951AAF.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 29.8 MB link
ENCFF969WSQ ENCFF969WSQ.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 27.4 MB link
ENCFF372IRX ENCFF372IRX.tsv tsv (transcript quantifications); assembly: hg19; genome annotation: V19 transcript quantifications hg19 24.9 MB link
ENCFF774RIQ ENCFF774RIQ.tsv tsv (transcript quantifications); assembly: hg19; genome annotation: V19 transcript quantifications hg19 24.9 MB link