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ENCSR457WBK

ENCSR ENCODE
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RNA-seq on HepG2 cells treated with an shRNA knockdown against NUP35. (NUP35_BGHLV27)

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

Summary

shRNA RNA-seq of NUP35 in Homo sapiens HepG2 expressing RNAi targeting H. sapiens NUP35

Overall Design

RNA-seq on HepG2 cells treated with an shRNA knockdown against NUP35. (NUP35_BGHLV27)

Analysis

View Data Processing
Analysis page is available for ENCSR457WBK.

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: 194.2 GB
Assay: shRNA RNA-seq
Target: NUP35
Biosample: Homo sapiens HepG2 expressing RNAi targeting H. sapiens NUP35
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
ENCFF598FFY ENCFF598FFY.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 7.0 GB link
ENCFF746QLL ENCFF746QLL.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 8.4 GB link
ENCFF881QUW ENCFF881QUW.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 11.1 GB link
ENCFF931LIF ENCFF931LIF.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 9.2 GB link
ENCFF554GDY ENCFF554GDY.bam bam (alignments); assembly: GRCh38; genome annotation: V29 alignments GRCh38 8.4 GB link
ENCFF771LTT ENCFF771LTT.bam bam (alignments); assembly: GRCh38; genome annotation: V29 alignments GRCh38 11.1 GB link
ENCFF066VPP ENCFF066VPP.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 10.8 GB link
ENCFF222TBT ENCFF222TBT.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 9.1 GB link
ENCFF261DTU ENCFF261DTU.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 8.2 GB link
ENCFF537EKO ENCFF537EKO.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 6.9 GB link
ENCFF930HSH ENCFF930HSH.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 6.9 GB link
ENCFF941QUJ ENCFF941QUJ.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 9.1 GB link
ENCFF620FWJ ENCFF620FWJ.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V24 transcriptome alignments GRCh38 8.7 GB link
ENCFF735DQE ENCFF735DQE.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V24 transcriptome alignments GRCh38 11.6 GB link
ENCFF505BDU ENCFF505BDU.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V29 transcriptome alignments GRCh38 13.0 GB link
ENCFF836SIX ENCFF836SIX.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V29 transcriptome alignments GRCh38 9.8 GB link
ENCFF840PKH ENCFF840PKH.bam bam (transcriptome alignments); assembly: hg19; genome annotation: V19 transcriptome alignments hg19 11.6 GB link
ENCFF926KAE ENCFF926KAE.bam bam (transcriptome alignments); assembly: hg19; genome annotation: V19 transcriptome alignments hg19 8.7 GB link
ENCFF044PPY ENCFF044PPY.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 112.3 MB link
ENCFF201WSU ENCFF201WSU.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 76.9 MB link
ENCFF625WGQ ENCFF625WGQ.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 95.2 MB link
ENCFF729ZEQ ENCFF729ZEQ.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 90.6 MB link
ENCFF077DQZ ENCFF077DQZ.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V29 minus strand signal of all reads GRCh38 95.2 MB link
ENCFF239JXL ENCFF239JXL.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V29 minus strand signal of all reads GRCh38 112.3 MB link
ENCFF199GCA ENCFF199GCA.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 75.5 MB link
ENCFF214UWC ENCFF214UWC.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 78.9 MB link
ENCFF326PGC ENCFF326PGC.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 89.3 MB link
ENCFF560QDQ ENCFF560QDQ.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 95.1 MB link
ENCFF662DXO ENCFF662DXO.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 111.3 MB link
ENCFF778ORK ENCFF778ORK.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 91.5 MB link
ENCFF147ZVM ENCFF147ZVM.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 72.1 MB link
ENCFF346TXF ENCFF346TXF.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 84.7 MB link
ENCFF358DLP ENCFF358DLP.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 84.6 MB link
ENCFF628JAP ENCFF628JAP.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 98.5 MB link
ENCFF315KTT ENCFF315KTT.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 minus strand signal of unique reads GRCh38 98.5 MB link
ENCFF515IIT ENCFF515IIT.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 minus strand signal of unique reads GRCh38 84.4 MB link
ENCFF181FRM ENCFF181FRM.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 69.8 MB link
ENCFF463BWE ENCFF463BWE.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 85.5 MB link
ENCFF594PKW ENCFF594PKW.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 98.5 MB link
ENCFF723EJB ENCFF723EJB.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 84.0 MB link
ENCFF837VFB ENCFF837VFB.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 82.6 MB link
ENCFF922EIO ENCFF922EIO.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 72.7 MB link
ENCFF267NSU ENCFF267NSU.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 77.7 MB link
ENCFF397EDB ENCFF397EDB.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 96.0 MB link
ENCFF449BVI ENCFF449BVI.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 91.7 MB link
ENCFF913TVD ENCFF913TVD.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 113.5 MB link
ENCFF254HPW ENCFF254HPW.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V29 plus strand signal of all reads GRCh38 96.0 MB link
ENCFF485QYR ENCFF485QYR.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V29 plus strand signal of all reads GRCh38 113.5 MB link
ENCFF199ILN ENCFF199ILN.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 95.8 MB link
ENCFF212XGG ENCFF212XGG.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 76.5 MB link
ENCFF389YRE ENCFF389YRE.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 79.8 MB link
ENCFF481JBH ENCFF481JBH.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 92.8 MB link
ENCFF487HDY ENCFF487HDY.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 112.3 MB link
ENCFF640CET ENCFF640CET.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 90.6 MB link
ENCFF175ALF ENCFF175ALF.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 100.5 MB link
ENCFF747SYF ENCFF747SYF.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 73.4 MB link
ENCFF784YYK ENCFF784YYK.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 86.1 MB link
ENCFF785ISQ ENCFF785ISQ.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 86.4 MB link
ENCFF439YUE ENCFF439YUE.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 plus strand signal of unique reads GRCh38 85.8 MB link
ENCFF893IHQ ENCFF893IHQ.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 plus strand signal of unique reads GRCh38 100.5 MB link
ENCFF258RRB ENCFF258RRB.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 84.4 MB link
ENCFF400YCO ENCFF400YCO.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 85.5 MB link
ENCFF625PRM ENCFF625PRM.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 74.1 MB link
ENCFF697NPN ENCFF697NPN.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 71.3 MB link
ENCFF774UUT ENCFF774UUT.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 87.3 MB link
ENCFF977SGZ ENCFF977SGZ.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 100.5 MB link
ENCFF190HYE ENCFF190HYE.fastq fastq (reads) reads 5.8 GB link
ENCFF280HQF ENCFF280HQF.fastq fastq (reads) reads 4.4 GB link
ENCFF575HWB ENCFF575HWB.fastq fastq (reads) reads 4.5 GB link
ENCFF799NDX ENCFF799NDX.fastq fastq (reads) reads 5.9 GB link
ENCFF591VNS ENCFF591VNS.tar tar (differential splicing quantifications); assembly: hg19; genome annotation: V19 differential splicing quantifications hg19 16.3 MB link
ENCFF929PEU ENCFF929PEU.tar tar (differential splicing quantifications); assembly: hg19; genome annotation: V19 differential splicing quantifications hg19 3.3 MB link
ENCFF999TPX ENCFF999TPX.tar tar (differential splicing quantifications); assembly: hg19; genome annotation: V19 differential splicing quantifications hg19 3.8 MB link
ENCFF247YNX ENCFF247YNX.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 5.6 MB link
ENCFF463MPC ENCFF463MPC.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 4.2 MB link
ENCFF511CYH ENCFF511CYH.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 2.0 MB link
ENCFF651XXR ENCFF651XXR.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 2.9 MB link
ENCFF992EJK ENCFF992EJK.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 1.7 MB link
ENCFF083AKD ENCFF083AKD.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V24 gene quantifications GRCh38 9.5 MB link
ENCFF498IGB ENCFF498IGB.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V24 gene quantifications GRCh38 9.5 MB link
ENCFF129GOG ENCFF129GOG.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V29 gene quantifications GRCh38 10.4 MB link
ENCFF883OMZ ENCFF883OMZ.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V29 gene quantifications GRCh38 10.4 MB link
ENCFF303VHB ENCFF303VHB.tsv tsv (gene quantifications); assembly: hg19; genome annotation: V19 gene quantifications hg19 9.1 MB link
ENCFF493FUL ENCFF493FUL.tsv tsv (gene quantifications); assembly: hg19; genome annotation: V19 gene quantifications hg19 9.1 MB link
ENCFF104ZGJ ENCFF104ZGJ.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V24 transcript quantifications GRCh38 25.4 MB link
ENCFF779KWR ENCFF779KWR.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V24 transcript quantifications GRCh38 25.4 MB link
ENCFF050XKU ENCFF050XKU.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 27.4 MB link
ENCFF210FWS ENCFF210FWS.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 27.5 MB link
ENCFF352IEN ENCFF352IEN.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 29.9 MB link
ENCFF917ERG ENCFF917ERG.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 29.9 MB link
ENCFF464SYH ENCFF464SYH.tsv tsv (transcript quantifications); assembly: hg19; genome annotation: V19 transcript quantifications hg19 25.0 MB link
ENCFF928OET ENCFF928OET.tsv tsv (transcript quantifications); assembly: hg19; genome annotation: V19 transcript quantifications hg19 25.0 MB link