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ENCSR208GPE

ENCSR ENCODE
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RNA-seq on K562 cells treated with an shRNA knockdown against DDX1. (DDX1_BGKLV24)

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

Summary

shRNA RNA-seq of DDX1 in Homo sapiens K562 expressing RNAi targeting H. sapiens DDX1

Overall Design

RNA-seq on K562 cells treated with an shRNA knockdown against DDX1. (DDX1_BGKLV24)

Analysis

View Data Processing
Analysis page is available for ENCSR208GPE.

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: 70.0 GB
Assay: shRNA RNA-seq
Target: DDX1
Biosample: Homo sapiens K562 expressing RNAi targeting H. sapiens DDX1
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
ENCFF003MPA ENCFF003MPA.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 2.6 GB link
ENCFF382ZLG ENCFF382ZLG.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 3.0 GB link
ENCFF384PMZ ENCFF384PMZ.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 3.0 GB link
ENCFF642PWD ENCFF642PWD.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 3.5 GB link
ENCFF106LGM ENCFF106LGM.bam bam (alignments); assembly: GRCh38; genome annotation: V29 alignments GRCh38 3.0 GB link
ENCFF948ZOO ENCFF948ZOO.bam bam (alignments); assembly: GRCh38; genome annotation: V29 alignments GRCh38 3.5 GB link
ENCFF017QVW ENCFF017QVW.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 3.0 GB link
ENCFF083FIL ENCFF083FIL.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 2.6 GB link
ENCFF119LVD ENCFF119LVD.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 2.9 GB link
ENCFF330IVL ENCFF330IVL.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 2.9 GB link
ENCFF539QKE ENCFF539QKE.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 3.4 GB link
ENCFF783EBM ENCFF783EBM.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 2.6 GB link
ENCFF566LDL ENCFF566LDL.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V24 transcriptome alignments GRCh38 4.1 GB link
ENCFF737ULL ENCFF737ULL.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V24 transcriptome alignments GRCh38 3.6 GB link
ENCFF056GQJ ENCFF056GQJ.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V29 transcriptome alignments GRCh38 4.6 GB link
ENCFF169ZSF ENCFF169ZSF.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V29 transcriptome alignments GRCh38 4.0 GB link
ENCFF193SWU ENCFF193SWU.bam bam (transcriptome alignments); assembly: hg19; genome annotation: V19 transcriptome alignments hg19 4.1 GB link
ENCFF862KJJ ENCFF862KJJ.bam bam (transcriptome alignments); assembly: hg19; genome annotation: V19 transcriptome alignments hg19 3.5 GB link
ENCFF056IZS ENCFF056IZS.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 72.3 MB link
ENCFF385BST ENCFF385BST.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 54.4 MB link
ENCFF516FLP ENCFF516FLP.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 60.4 MB link
ENCFF827XEI ENCFF827XEI.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 65.2 MB link
ENCFF302EUQ ENCFF302EUQ.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V29 minus strand signal of all reads GRCh38 72.4 MB link
ENCFF770LFG ENCFF770LFG.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V29 minus strand signal of all reads GRCh38 60.4 MB link
ENCFF305VRM ENCFF305VRM.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 62.0 MB link
ENCFF488AVS ENCFF488AVS.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 71.0 MB link
ENCFF540HJZ ENCFF540HJZ.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 65.8 MB link
ENCFF738TNX ENCFF738TNX.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 60.2 MB link
ENCFF758FLI ENCFF758FLI.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 51.1 MB link
ENCFF909AED ENCFF909AED.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 55.2 MB link
ENCFF012HGO ENCFF012HGO.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 64.1 MB link
ENCFF258GMR ENCFF258GMR.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 50.5 MB link
ENCFF665BRZ ENCFF665BRZ.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 60.4 MB link
ENCFF780WFQ ENCFF780WFQ.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 53.2 MB link
ENCFF588CFU ENCFF588CFU.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 minus strand signal of unique reads GRCh38 53.7 MB link
ENCFF744IFB ENCFF744IFB.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 minus strand signal of unique reads GRCh38 63.6 MB link
ENCFF035PTV ENCFF035PTV.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 53.6 MB link
ENCFF037ASI ENCFF037ASI.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 50.8 MB link
ENCFF160GKA ENCFF160GKA.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 57.0 MB link
ENCFF415RAU ENCFF415RAU.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 64.0 MB link
ENCFF723XNO ENCFF723XNO.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 47.2 MB link
ENCFF878GXF ENCFF878GXF.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 60.0 MB link
ENCFF125CWE ENCFF125CWE.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 61.3 MB link
ENCFF460YPK ENCFF460YPK.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 55.1 MB link
ENCFF580GWL ENCFF580GWL.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 66.1 MB link
ENCFF678YBG ENCFF678YBG.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 73.3 MB link
ENCFF375XFI ENCFF375XFI.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V29 plus strand signal of all reads GRCh38 61.3 MB link
ENCFF997SXJ ENCFF997SXJ.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V29 plus strand signal of all reads GRCh38 73.5 MB link
ENCFF142FYN ENCFF142FYN.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 63.3 MB link
ENCFF236OSM ENCFF236OSM.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 67.0 MB link
ENCFF237DUH ENCFF237DUH.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 72.0 MB link
ENCFF254GBV ENCFF254GBV.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 56.2 MB link
ENCFF468TXX ENCFF468TXX.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 61.1 MB link
ENCFF522VZO ENCFF522VZO.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 52.1 MB link
ENCFF029XKQ ENCFF029XKQ.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 51.6 MB link
ENCFF075QLI ENCFF075QLI.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 54.5 MB link
ENCFF184RKO ENCFF184RKO.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 65.7 MB link
ENCFF322SLF ENCFF322SLF.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 61.8 MB link
ENCFF727TPR ENCFF727TPR.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 plus strand signal of unique reads GRCh38 65.1 MB link
ENCFF766ODP ENCFF766ODP.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 plus strand signal of unique reads GRCh38 55.0 MB link
ENCFF081WOU ENCFF081WOU.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 61.7 MB link
ENCFF485DMS ENCFF485DMS.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 48.6 MB link
ENCFF735RUU ENCFF735RUU.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 58.7 MB link
ENCFF804DHN ENCFF804DHN.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 55.1 MB link
ENCFF841UJK ENCFF841UJK.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 52.1 MB link
ENCFF908VQT ENCFF908VQT.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 65.7 MB link
ENCFF127FKO ENCFF127FKO.fastq fastq (reads) reads 1.8 GB link
ENCFF184FWX ENCFF184FWX.fastq fastq (reads) reads 1.9 GB link
ENCFF461JUR ENCFF461JUR.fastq fastq (reads) reads 1.7 GB link
ENCFF982RUK ENCFF982RUK.fastq fastq (reads) reads 1.6 GB link
ENCFF235VSZ ENCFF235VSZ.tar tar (differential splicing quantifications); assembly: hg19; genome annotation: V19 differential splicing quantifications hg19 3.2 MB link
ENCFF246KBS ENCFF246KBS.tar tar (differential splicing quantifications); assembly: hg19; genome annotation: V19 differential splicing quantifications hg19 12.9 MB link
ENCFF280LRA ENCFF280LRA.tar tar (differential splicing quantifications); assembly: hg19; genome annotation: V19 differential splicing quantifications hg19 2.9 MB link
ENCFF083XAJ ENCFF083XAJ.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 5.4 MB link
ENCFF167AUM ENCFF167AUM.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 4.0 MB link
ENCFF249PHP ENCFF249PHP.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 2.7 MB link
ENCFF738XKM ENCFF738XKM.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 1.9 MB link
ENCFF888WFP ENCFF888WFP.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 1.8 MB link
ENCFF601FFK ENCFF601FFK.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V24 gene quantifications GRCh38 9.4 MB link
ENCFF756IOS ENCFF756IOS.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V24 gene quantifications GRCh38 9.4 MB link
ENCFF383VZM ENCFF383VZM.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V29 gene quantifications GRCh38 10.4 MB link
ENCFF651KLQ ENCFF651KLQ.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V29 gene quantifications GRCh38 10.4 MB link
ENCFF551GXQ ENCFF551GXQ.tsv tsv (gene quantifications); assembly: hg19; genome annotation: V19 gene quantifications hg19 9.1 MB link
ENCFF678HHM ENCFF678HHM.tsv tsv (gene quantifications); assembly: hg19; genome annotation: V19 gene quantifications hg19 9.1 MB link
ENCFF491BAM ENCFF491BAM.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V24 transcript quantifications GRCh38 25.3 MB link
ENCFF925MFO ENCFF925MFO.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V24 transcript quantifications GRCh38 25.3 MB link
ENCFF090BXT ENCFF090BXT.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 27.2 MB link
ENCFF118QDQ ENCFF118QDQ.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 27.3 MB link
ENCFF545XKC ENCFF545XKC.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 29.8 MB link
ENCFF985QIW ENCFF985QIW.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 29.8 MB link
ENCFF193XZI ENCFF193XZI.tsv tsv (transcript quantifications); assembly: hg19; genome annotation: V19 transcript quantifications hg19 24.9 MB link
ENCFF465RJA ENCFF465RJA.tsv tsv (transcript quantifications); assembly: hg19; genome annotation: V19 transcript quantifications hg19 24.9 MB link