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ENCSR810FHY

ENCSR ENCODE
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RNA-seq on K562 cells treated with an shRNA knockdown against UPF2. (UPF2_BGKLV21-B)

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

Summary

shRNA RNA-seq of UPF2 in Homo sapiens K562 expressing RNAi targeting H. sapiens UPF2

Overall Design

RNA-seq on K562 cells treated with an shRNA knockdown against UPF2. (UPF2_BGKLV21-B)

Analysis

View Data Processing
Analysis page is available for ENCSR810FHY.

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: 93.5 GB
Assay: shRNA RNA-seq
Target: UPF2
Biosample: Homo sapiens K562 expressing RNAi targeting H. sapiens UPF2
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
ENCFF345BGU ENCFF345BGU.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 3.3 GB link
ENCFF477PXW ENCFF477PXW.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 4.4 GB link
ENCFF505YOD ENCFF505YOD.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 3.5 GB link
ENCFF583XQP ENCFF583XQP.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 4.2 GB link
ENCFF709CYO ENCFF709CYO.bam bam (alignments); assembly: GRCh38; genome annotation: V29 alignments GRCh38 4.2 GB link
ENCFF828IFS ENCFF828IFS.bam bam (alignments); assembly: GRCh38; genome annotation: V29 alignments GRCh38 4.4 GB link
ENCFF116UZG ENCFF116UZG.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 3.3 GB link
ENCFF182AMB ENCFF182AMB.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 4.3 GB link
ENCFF397BWB ENCFF397BWB.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 3.4 GB link
ENCFF417DDZ ENCFF417DDZ.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 3.4 GB link
ENCFF779RLG ENCFF779RLG.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 4.1 GB link
ENCFF990XTX ENCFF990XTX.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 3.3 GB link
ENCFF130MNN ENCFF130MNN.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V24 transcriptome alignments GRCh38 5.3 GB link
ENCFF302XGD ENCFF302XGD.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V24 transcriptome alignments GRCh38 5.4 GB link
ENCFF560XAB ENCFF560XAB.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V29 transcriptome alignments GRCh38 6.2 GB link
ENCFF967QZR ENCFF967QZR.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V29 transcriptome alignments GRCh38 6.1 GB link
ENCFF077KWZ ENCFF077KWZ.bam bam (transcriptome alignments); assembly: hg19; genome annotation: V19 transcriptome alignments hg19 5.3 GB link
ENCFF545EJL ENCFF545EJL.bam bam (transcriptome alignments); assembly: hg19; genome annotation: V19 transcriptome alignments hg19 5.3 GB link
ENCFF327TCW ENCFF327TCW.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 106.3 MB link
ENCFF592LBR ENCFF592LBR.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 95.8 MB link
ENCFF689BNS ENCFF689BNS.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 100.3 MB link
ENCFF783WAW ENCFF783WAW.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 89.4 MB link
ENCFF020CNG ENCFF020CNG.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V29 minus strand signal of all reads GRCh38 100.4 MB link
ENCFF495VJK ENCFF495VJK.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V29 minus strand signal of all reads GRCh38 106.3 MB link
ENCFF219IQC ENCFF219IQC.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 91.5 MB link
ENCFF636NUC ENCFF636NUC.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 93.1 MB link
ENCFF650FWW ENCFF650FWW.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 87.6 MB link
ENCFF763IGM ENCFF763IGM.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 96.2 MB link
ENCFF900RBC ENCFF900RBC.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 105.5 MB link
ENCFF970WIS ENCFF970WIS.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 98.2 MB link
ENCFF594CMO ENCFF594CMO.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 87.9 MB link
ENCFF619UFX ENCFF619UFX.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 87.7 MB link
ENCFF786LVQ ENCFF786LVQ.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 82.7 MB link
ENCFF920QRD ENCFF920QRD.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 94.5 MB link
ENCFF459FEX ENCFF459FEX.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 minus strand signal of unique reads GRCh38 94.4 MB link
ENCFF724HZR ENCFF724HZR.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 minus strand signal of unique reads GRCh38 88.7 MB link
ENCFF063CBX ENCFF063CBX.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 85.7 MB link
ENCFF231SCI ENCFF231SCI.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 88.2 MB link
ENCFF309EVO ENCFF309EVO.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 83.0 MB link
ENCFF670PZQ ENCFF670PZQ.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 93.2 MB link
ENCFF739IRO ENCFF739IRO.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 80.3 MB link
ENCFF974HAM ENCFF974HAM.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 88.5 MB link
ENCFF601LGH ENCFF601LGH.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 101.6 MB link
ENCFF725YET ENCFF725YET.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 97.2 MB link
ENCFF865OER ENCFF865OER.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 90.6 MB link
ENCFF870TKH ENCFF870TKH.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 107.8 MB link
ENCFF027UUU ENCFF027UUU.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V29 plus strand signal of all reads GRCh38 107.8 MB link
ENCFF413UPC ENCFF413UPC.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V29 plus strand signal of all reads GRCh38 101.7 MB link
ENCFF350RAC ENCFF350RAC.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 95.1 MB link
ENCFF540RZW ENCFF540RZW.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 99.5 MB link
ENCFF677NCC ENCFF677NCC.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 93.1 MB link
ENCFF728NYQ ENCFF728NYQ.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 98.1 MB link
ENCFF755RMR ENCFF755RMR.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 107.1 MB link
ENCFF944VLT ENCFF944VLT.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 89.2 MB link
ENCFF282FXJ ENCFF282FXJ.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 84.5 MB link
ENCFF406LCB ENCFF406LCB.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 89.8 MB link
ENCFF864RVN ENCFF864RVN.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 96.9 MB link
ENCFF901VVJ ENCFF901VVJ.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 90.0 MB link
ENCFF145XGQ ENCFF145XGQ.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 plus strand signal of unique reads GRCh38 96.7 MB link
ENCFF938PYH ENCFF938PYH.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 plus strand signal of unique reads GRCh38 90.7 MB link
ENCFF081NXV ENCFF081NXV.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 88.3 MB link
ENCFF156CJJ ENCFF156CJJ.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 95.7 MB link
ENCFF222PEE ENCFF222PEE.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 90.8 MB link
ENCFF240URE ENCFF240URE.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 82.6 MB link
ENCFF335GYQ ENCFF335GYQ.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 90.7 MB link
ENCFF979KZZ ENCFF979KZZ.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 85.1 MB link
ENCFF186PXP ENCFF186PXP.fastq fastq (reads) reads 2.4 GB link
ENCFF892SIK ENCFF892SIK.fastq fastq (reads) reads 2.3 GB link
ENCFF941MVX ENCFF941MVX.fastq fastq (reads) reads 2.3 GB link
ENCFF949APM ENCFF949APM.fastq fastq (reads) reads 2.4 GB link
ENCFF204KSY ENCFF204KSY.tar tar (differential splicing quantifications); assembly: hg19; genome annotation: V19 differential splicing quantifications hg19 4.0 MB link
ENCFF370MSX ENCFF370MSX.tar tar (differential splicing quantifications); assembly: hg19; genome annotation: V19 differential splicing quantifications hg19 4.8 MB link
ENCFF616LII ENCFF616LII.tar tar (differential splicing quantifications); assembly: hg19; genome annotation: V19 differential splicing quantifications hg19 17.0 MB link
ENCFF282ZUP ENCFF282ZUP.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 5.5 MB link
ENCFF311QJP ENCFF311QJP.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 2.8 MB link
ENCFF371GCK ENCFF371GCK.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 1.9 MB link
ENCFF637MRZ ENCFF637MRZ.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 1.7 MB link
ENCFF829PHK ENCFF829PHK.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 4.2 MB link
ENCFF513SVU ENCFF513SVU.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V24 gene quantifications GRCh38 9.5 MB link
ENCFF697NZP ENCFF697NZP.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V24 gene quantifications GRCh38 9.5 MB link
ENCFF534YWO ENCFF534YWO.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V29 gene quantifications GRCh38 10.4 MB link
ENCFF839OSJ ENCFF839OSJ.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V29 gene quantifications GRCh38 10.4 MB link
ENCFF504GEQ ENCFF504GEQ.tsv tsv (gene quantifications); assembly: hg19; genome annotation: V19 gene quantifications hg19 9.1 MB link
ENCFF567TFK ENCFF567TFK.tsv tsv (gene quantifications); assembly: hg19; genome annotation: V19 gene quantifications hg19 9.1 MB link
ENCFF289HXW ENCFF289HXW.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V24 transcript quantifications GRCh38 25.3 MB link
ENCFF942JPV ENCFF942JPV.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V24 transcript quantifications GRCh38 25.3 MB link
ENCFF021FBV ENCFF021FBV.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 29.8 MB link
ENCFF261PXK ENCFF261PXK.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 29.8 MB link
ENCFF281NTB ENCFF281NTB.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 27.4 MB link
ENCFF671ETA ENCFF671ETA.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 27.3 MB link
ENCFF199ZWW ENCFF199ZWW.tsv tsv (transcript quantifications); assembly: hg19; genome annotation: V19 transcript quantifications hg19 24.9 MB link
ENCFF215DZO ENCFF215DZO.tsv tsv (transcript quantifications); assembly: hg19; genome annotation: V19 transcript quantifications hg19 24.9 MB link