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ENCSR453HKS

ENCSR ENCODE
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RNA-seq on K562 cells treated with an shRNA knockdown against XPO5. (XPO5_BGKLV28)

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

Summary

shRNA RNA-seq of XPO5 in Homo sapiens K562 expressing RNAi targeting H. sapiens XPO5

Overall Design

RNA-seq on K562 cells treated with an shRNA knockdown against XPO5. (XPO5_BGKLV28)

Analysis

View Data Processing
Analysis page is available for ENCSR453HKS.

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: 111.1 GB
Assay: shRNA RNA-seq
Target: XPO5
Biosample: Homo sapiens K562 expressing RNAi targeting H. sapiens XPO5
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
ENCFF174KMG ENCFF174KMG.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 4.5 GB link
ENCFF196SQK ENCFF196SQK.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 5.5 GB link
ENCFF291XKX ENCFF291XKX.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 4.6 GB link
ENCFF721WCK ENCFF721WCK.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 5.5 GB link
ENCFF316ZPA ENCFF316ZPA.bam bam (alignments); assembly: GRCh38; genome annotation: V29 alignments GRCh38 5.6 GB link
ENCFF769NGO ENCFF769NGO.bam bam (alignments); assembly: GRCh38; genome annotation: V29 alignments GRCh38 5.5 GB link
ENCFF037CZQ ENCFF037CZQ.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 4.3 GB link
ENCFF054AOA ENCFF054AOA.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 5.2 GB link
ENCFF260LWA ENCFF260LWA.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 5.3 GB link
ENCFF437XUU ENCFF437XUU.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 4.5 GB link
ENCFF485JUE ENCFF485JUE.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 4.3 GB link
ENCFF779PNB ENCFF779PNB.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 4.5 GB link
ENCFF273BUV ENCFF273BUV.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V24 transcriptome alignments GRCh38 6.0 GB link
ENCFF903QZU ENCFF903QZU.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V24 transcriptome alignments GRCh38 5.7 GB link
ENCFF475HEF ENCFF475HEF.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V29 transcriptome alignments GRCh38 6.8 GB link
ENCFF592UJA ENCFF592UJA.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V29 transcriptome alignments GRCh38 6.4 GB link
ENCFF213WRS ENCFF213WRS.bam bam (transcriptome alignments); assembly: hg19; genome annotation: V19 transcriptome alignments hg19 6.0 GB link
ENCFF774UWV ENCFF774UWV.bam bam (transcriptome alignments); assembly: hg19; genome annotation: V19 transcriptome alignments hg19 5.6 GB link
ENCFF121BCY ENCFF121BCY.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 79.0 MB link
ENCFF678QIV ENCFF678QIV.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 78.4 MB link
ENCFF827ZVT ENCFF827ZVT.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 91.6 MB link
ENCFF907MMP ENCFF907MMP.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 90.9 MB link
ENCFF214WIU ENCFF214WIU.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V29 minus strand signal of all reads GRCh38 90.9 MB link
ENCFF444JWS ENCFF444JWS.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V29 minus strand signal of all reads GRCh38 91.6 MB link
ENCFF003MVF ENCFF003MVF.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 89.8 MB link
ENCFF188RRK ENCFF188RRK.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 76.0 MB link
ENCFF272DXH ENCFF272DXH.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 79.3 MB link
ENCFF448CWR ENCFF448CWR.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 76.1 MB link
ENCFF808QQZ ENCFF808QQZ.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 79.7 MB link
ENCFF813VFB ENCFF813VFB.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 90.0 MB link
ENCFF226LNY ENCFF226LNY.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 80.0 MB link
ENCFF570YAW ENCFF570YAW.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 72.4 MB link
ENCFF628FGD ENCFF628FGD.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 73.0 MB link
ENCFF678PFM ENCFF678PFM.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 78.9 MB link
ENCFF041ZLE ENCFF041ZLE.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 minus strand signal of unique reads GRCh38 79.9 MB link
ENCFF457WZB ENCFF457WZB.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 minus strand signal of unique reads GRCh38 79.4 MB link
ENCFF160AJB ENCFF160AJB.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 79.3 MB link
ENCFF187JGX ENCFF187JGX.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 79.2 MB link
ENCFF356CHE ENCFF356CHE.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 72.6 MB link
ENCFF581MAL ENCFF581MAL.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 69.0 MB link
ENCFF839WCG ENCFF839WCG.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 69.8 MB link
ENCFF935QNK ENCFF935QNK.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 72.5 MB link
ENCFF069GFC ENCFF069GFC.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 80.1 MB link
ENCFF164ISW ENCFF164ISW.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 91.9 MB link
ENCFF228CIU ENCFF228CIU.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 92.8 MB link
ENCFF906LTJ ENCFF906LTJ.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 79.3 MB link
ENCFF732EWE ENCFF732EWE.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V29 plus strand signal of all reads GRCh38 92.8 MB link
ENCFF889WPQ ENCFF889WPQ.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V29 plus strand signal of all reads GRCh38 91.9 MB link
ENCFF355CQY ENCFF355CQY.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 77.4 MB link
ENCFF379OAQ ENCFF379OAQ.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 77.8 MB link
ENCFF515NBR ENCFF515NBR.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 91.0 MB link
ENCFF563DCP ENCFF563DCP.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 81.2 MB link
ENCFF874YYT ENCFF874YYT.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 80.7 MB link
ENCFF907HKI ENCFF907HKI.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 91.1 MB link
ENCFF368SSL ENCFF368SSL.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 74.5 MB link
ENCFF679HGP ENCFF679HGP.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 80.7 MB link
ENCFF726VIV ENCFF726VIV.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 74.0 MB link
ENCFF812ARP ENCFF812ARP.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 81.6 MB link
ENCFF592MGW ENCFF592MGW.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 plus strand signal of unique reads GRCh38 81.7 MB link
ENCFF986KXS ENCFF986KXS.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 plus strand signal of unique reads GRCh38 81.1 MB link
ENCFF455TIP ENCFF455TIP.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 70.9 MB link
ENCFF592SZH ENCFF592SZH.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 74.4 MB link
ENCFF785YQJ ENCFF785YQJ.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 81.1 MB link
ENCFF923HGZ ENCFF923HGZ.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 74.4 MB link
ENCFF958CSB ENCFF958CSB.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 81.3 MB link
ENCFF979HVN ENCFF979HVN.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 71.6 MB link
ENCFF052PAR ENCFF052PAR.fastq fastq (reads) reads 2.8 GB link
ENCFF254DEP ENCFF254DEP.fastq fastq (reads) reads 2.8 GB link
ENCFF569JDC ENCFF569JDC.fastq fastq (reads) reads 2.9 GB link
ENCFF766GUZ ENCFF766GUZ.fastq fastq (reads) reads 2.9 GB link
ENCFF026NKB ENCFF026NKB.tar tar (differential splicing quantifications); assembly: hg19; genome annotation: V19 differential splicing quantifications hg19 3.7 MB link
ENCFF595SNA ENCFF595SNA.tar tar (differential splicing quantifications); assembly: hg19; genome annotation: V19 differential splicing quantifications hg19 4.6 MB link
ENCFF988VZR ENCFF988VZR.tar tar (differential splicing quantifications); assembly: hg19; genome annotation: V19 differential splicing quantifications hg19 15.8 MB link
ENCFF070OXW ENCFF070OXW.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 4.3 MB link
ENCFF281INK ENCFF281INK.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 1.9 MB link
ENCFF554LYK ENCFF554LYK.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 5.5 MB link
ENCFF634RGS ENCFF634RGS.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 2.9 MB link
ENCFF939RFQ ENCFF939RFQ.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 1.7 MB link
ENCFF017JIH ENCFF017JIH.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V24 gene quantifications GRCh38 9.5 MB link
ENCFF748UAT ENCFF748UAT.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V24 gene quantifications GRCh38 9.5 MB link
ENCFF724QJC ENCFF724QJC.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V29 gene quantifications GRCh38 10.4 MB link
ENCFF767OCD ENCFF767OCD.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V29 gene quantifications GRCh38 10.4 MB link
ENCFF077MJK ENCFF077MJK.tsv tsv (gene quantifications); assembly: hg19; genome annotation: V19 gene quantifications hg19 9.1 MB link
ENCFF393VSN ENCFF393VSN.tsv tsv (gene quantifications); assembly: hg19; genome annotation: V19 gene quantifications hg19 9.1 MB link
ENCFF429QFX ENCFF429QFX.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V24 transcript quantifications GRCh38 25.3 MB link
ENCFF837KKP ENCFF837KKP.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V24 transcript quantifications GRCh38 25.3 MB link
ENCFF267VOZ ENCFF267VOZ.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 27.4 MB link
ENCFF437QPU ENCFF437QPU.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 27.4 MB link
ENCFF588PYP ENCFF588PYP.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 29.8 MB link
ENCFF857PSQ ENCFF857PSQ.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 29.8 MB link
ENCFF450PIM ENCFF450PIM.tsv tsv (transcript quantifications); assembly: hg19; genome annotation: V19 transcript quantifications hg19 24.9 MB link
ENCFF692QUH ENCFF692QUH.tsv tsv (transcript quantifications); assembly: hg19; genome annotation: V19 transcript quantifications hg19 24.9 MB link