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ENCSR995RPB

ENCSR ENCODE
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shRNA knockdown against SUPV3L1 in HepG2 cells followed by RNA-seq. (SUPV3L1_BGHLV17)

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

Summary

shRNA RNA-seq of SUPV3L1 in Homo sapiens HepG2 expressing RNAi targeting H. sapiens SUPV3L1

Overall Design

shRNA knockdown against SUPV3L1 in HepG2 cells followed by RNA-seq. (SUPV3L1_BGHLV17)

Analysis

View Data Processing
Analysis page is available for ENCSR995RPB.

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: 131.2 GB
Assay: shRNA RNA-seq
Target: SUPV3L1
Biosample: Homo sapiens HepG2 expressing RNAi targeting H. sapiens SUPV3L1
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
ENCFF473YSD ENCFF473YSD.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 5.9 GB link
ENCFF624NBF ENCFF624NBF.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 5.3 GB link
ENCFF843KJF ENCFF843KJF.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 7.0 GB link
ENCFF990SFW ENCFF990SFW.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 4.5 GB link
ENCFF012QGJ ENCFF012QGJ.bam bam (alignments); assembly: GRCh38; genome annotation: V29 alignments GRCh38 5.3 GB link
ENCFF963IEY ENCFF963IEY.bam bam (alignments); assembly: GRCh38; genome annotation: V29 alignments GRCh38 7.0 GB link
ENCFF078QOX ENCFF078QOX.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 5.8 GB link
ENCFF082CNV ENCFF082CNV.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 6.8 GB link
ENCFF192VFW ENCFF192VFW.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 4.4 GB link
ENCFF596TAC ENCFF596TAC.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 4.4 GB link
ENCFF719ZER ENCFF719ZER.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 5.8 GB link
ENCFF734OAK ENCFF734OAK.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 5.2 GB link
ENCFF072BGK ENCFF072BGK.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V24 transcriptome alignments GRCh38 6.4 GB link
ENCFF595YSP ENCFF595YSP.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V24 transcriptome alignments GRCh38 8.4 GB link
ENCFF503TWC ENCFF503TWC.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V29 transcriptome alignments GRCh38 9.4 GB link
ENCFF571IQW ENCFF571IQW.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V29 transcriptome alignments GRCh38 7.1 GB link
ENCFF682FOB ENCFF682FOB.bam bam (transcriptome alignments); assembly: hg19; genome annotation: V19 transcriptome alignments hg19 6.3 GB link
ENCFF757UIT ENCFF757UIT.bam bam (transcriptome alignments); assembly: hg19; genome annotation: V19 transcriptome alignments hg19 8.3 GB link
ENCFF083SAG ENCFF083SAG.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 89.1 MB link
ENCFF148QFK ENCFF148QFK.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 107.1 MB link
ENCFF858TEI ENCFF858TEI.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 96.1 MB link
ENCFF972UMU ENCFF972UMU.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 79.6 MB link
ENCFF633VXK ENCFF633VXK.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V29 minus strand signal of all reads GRCh38 107.1 MB link
ENCFF932WMK ENCFF932WMK.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V29 minus strand signal of all reads GRCh38 89.1 MB link
ENCFF205MAY ENCFF205MAY.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 97.0 MB link
ENCFF554KXS ENCFF554KXS.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 81.1 MB link
ENCFF602MEX ENCFF602MEX.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 105.4 MB link
ENCFF700VYO ENCFF700VYO.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 77.6 MB link
ENCFF949VAI ENCFF949VAI.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 87.9 MB link
ENCFF950KFK ENCFF950KFK.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 93.4 MB link
ENCFF172IUK ENCFF172IUK.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 74.9 MB link
ENCFF239DED ENCFF239DED.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 95.6 MB link
ENCFF587XHR ENCFF587XHR.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 80.2 MB link
ENCFF832XIT ENCFF832XIT.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 90.0 MB link
ENCFF044WAX ENCFF044WAX.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 minus strand signal of unique reads GRCh38 80.3 MB link
ENCFF118KLX ENCFF118KLX.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 minus strand signal of unique reads GRCh38 95.7 MB link
ENCFF117PAK ENCFF117PAK.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 90.2 MB link
ENCFF161DPV ENCFF161DPV.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 80.2 MB link
ENCFF312MTW ENCFF312MTW.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 87.5 MB link
ENCFF606GVH ENCFF606GVH.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 75.0 MB link
ENCFF646TQB ENCFF646TQB.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 96.0 MB link
ENCFF793STP ENCFF793STP.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 72.9 MB link
ENCFF064IYP ENCFF064IYP.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 97.7 MB link
ENCFF197UVH ENCFF197UVH.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 80.8 MB link
ENCFF205XEJ ENCFF205XEJ.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 90.4 MB link
ENCFF862YMX ENCFF862YMX.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 108.7 MB link
ENCFF015HPP ENCFF015HPP.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V29 plus strand signal of all reads GRCh38 90.4 MB link
ENCFF763UKF ENCFF763UKF.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V29 plus strand signal of all reads GRCh38 108.8 MB link
ENCFF288BKN ENCFF288BKN.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 107.0 MB link
ENCFF393IVU ENCFF393IVU.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 98.8 MB link
ENCFF465KZZ ENCFF465KZZ.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 89.2 MB link
ENCFF519WIE ENCFF519WIE.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 82.7 MB link
ENCFF649KPN ENCFF649KPN.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 95.2 MB link
ENCFF965CHB ENCFF965CHB.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 79.1 MB link
ENCFF029GUI ENCFF029GUI.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 82.2 MB link
ENCFF105VXB ENCFF105VXB.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 98.0 MB link
ENCFF299WGP ENCFF299WGP.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 92.1 MB link
ENCFF527HVC ENCFF527HVC.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 76.6 MB link
ENCFF356ENW ENCFF356ENW.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 plus strand signal of unique reads GRCh38 82.2 MB link
ENCFF816UAZ ENCFF816UAZ.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 plus strand signal of unique reads GRCh38 98.0 MB link
ENCFF051CWK ENCFF051CWK.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 76.9 MB link
ENCFF200JIY ENCFF200JIY.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 82.2 MB link
ENCFF614WRS ENCFF614WRS.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 92.5 MB link
ENCFF832QSD ENCFF832QSD.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 74.9 MB link
ENCFF838UMT ENCFF838UMT.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 98.5 MB link
ENCFF883AXR ENCFF883AXR.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 89.7 MB link
ENCFF118PYP ENCFF118PYP.fastq fastq (reads) reads 3.9 GB link
ENCFF235YCC ENCFF235YCC.fastq fastq (reads) reads 3.7 GB link
ENCFF417LQZ ENCFF417LQZ.fastq fastq (reads) reads 2.9 GB link
ENCFF624KNV ENCFF624KNV.fastq fastq (reads) reads 2.8 GB link
ENCFF313DFU ENCFF313DFU.tar tar (differential splicing quantifications); assembly: hg19; genome annotation: V19 differential splicing quantifications hg19 3.6 MB link
ENCFF760IOG ENCFF760IOG.tar tar (differential splicing quantifications); assembly: hg19; genome annotation: V19 differential splicing quantifications hg19 4.5 MB link
ENCFF775BFI ENCFF775BFI.tar tar (differential splicing quantifications); assembly: hg19; genome annotation: V19 differential splicing quantifications hg19 16.1 MB link
ENCFF226VZL ENCFF226VZL.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 2.0 MB link
ENCFF258NGR ENCFF258NGR.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 3.0 MB link
ENCFF339ZOK ENCFF339ZOK.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 5.7 MB link
ENCFF516RMD ENCFF516RMD.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 4.3 MB link
ENCFF556GXS ENCFF556GXS.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 1.8 MB link
ENCFF815NAE ENCFF815NAE.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V24 gene quantifications GRCh38 9.4 MB link
ENCFF827EGH ENCFF827EGH.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V24 gene quantifications GRCh38 9.5 MB link
ENCFF103ICB ENCFF103ICB.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V29 gene quantifications GRCh38 10.4 MB link
ENCFF684PVM ENCFF684PVM.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V29 gene quantifications GRCh38 10.4 MB link
ENCFF342YHK ENCFF342YHK.tsv tsv (gene quantifications); assembly: hg19; genome annotation: V19 gene quantifications hg19 9.1 MB link
ENCFF878MYE ENCFF878MYE.tsv tsv (gene quantifications); assembly: hg19; genome annotation: V19 gene quantifications hg19 9.1 MB link
ENCFF893FHR ENCFF893FHR.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V24 transcript quantifications GRCh38 25.3 MB link
ENCFF945KZX ENCFF945KZX.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V24 transcript quantifications GRCh38 25.3 MB link
ENCFF030UBV ENCFF030UBV.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 29.8 MB link
ENCFF273BKO ENCFF273BKO.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 29.8 MB link
ENCFF366ICU ENCFF366ICU.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 27.5 MB link
ENCFF791ZMT ENCFF791ZMT.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 27.4 MB link
ENCFF132YAV ENCFF132YAV.tsv tsv (transcript quantifications); assembly: hg19; genome annotation: V19 transcript quantifications hg19 24.9 MB link
ENCFF749PFW ENCFF749PFW.tsv tsv (transcript quantifications); assembly: hg19; genome annotation: V19 transcript quantifications hg19 24.9 MB link