← All datasets

ENCSR560RSZ

ENCSR ENCODE
Export SRA CSV View on ENCODE

shRNA knockdown against DDX52_06 in K562 cells followed by RNA-seq. (DDX52_BGKLV19)

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

Summary

shRNA RNA-seq of DDX52 in Homo sapiens K562 expressing RNAi targeting H. sapiens DDX52

Overall Design

shRNA knockdown against DDX52_06 in K562 cells followed by RNA-seq. (DDX52_BGKLV19)

Analysis

View Data Processing
Analysis page is available for ENCSR560RSZ.

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: 94.8 GB
Assay: shRNA RNA-seq
Target: DDX52
Biosample: Homo sapiens K562 expressing RNAi targeting H. sapiens DDX52
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
ENCFF398WLJ ENCFF398WLJ.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 4.2 GB link
ENCFF721UCM ENCFF721UCM.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 4.0 GB link
ENCFF749WVO ENCFF749WVO.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 3.5 GB link
ENCFF826NMS ENCFF826NMS.bam bam (alignments); assembly: GRCh38; genome annotation: V24 alignments GRCh38 4.8 GB link
ENCFF127KXZ ENCFF127KXZ.bam bam (alignments); assembly: GRCh38; genome annotation: V29 alignments GRCh38 4.8 GB link
ENCFF724MZM ENCFF724MZM.bam bam (alignments); assembly: GRCh38; genome annotation: V29 alignments GRCh38 4.2 GB link
ENCFF345SIU ENCFF345SIU.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 3.9 GB link
ENCFF429WFE ENCFF429WFE.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 3.9 GB link
ENCFF773SQT ENCFF773SQT.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 3.5 GB link
ENCFF807UXT ENCFF807UXT.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 3.5 GB link
ENCFF817BSA ENCFF817BSA.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 4.1 GB link
ENCFF935IWT ENCFF935IWT.bam bam (alignments); assembly: hg19; genome annotation: V19 alignments hg19 4.6 GB link
ENCFF671IES ENCFF671IES.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V24 transcriptome alignments GRCh38 5.5 GB link
ENCFF996OQB ENCFF996OQB.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V24 transcriptome alignments GRCh38 4.8 GB link
ENCFF562IQG ENCFF562IQG.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V29 transcriptome alignments GRCh38 6.2 GB link
ENCFF883BCP ENCFF883BCP.bam bam (transcriptome alignments); assembly: GRCh38; genome annotation: V29 transcriptome alignments GRCh38 5.4 GB link
ENCFF341GDK ENCFF341GDK.bam bam (transcriptome alignments); assembly: hg19; genome annotation: V19 transcriptome alignments hg19 4.8 GB link
ENCFF887MWJ ENCFF887MWJ.bam bam (transcriptome alignments); assembly: hg19; genome annotation: V19 transcriptome alignments hg19 5.4 GB link
ENCFF374VEA ENCFF374VEA.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 83.7 MB link
ENCFF595WMJ ENCFF595WMJ.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 89.1 MB link
ENCFF823GPW ENCFF823GPW.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 79.7 MB link
ENCFF951XGB ENCFF951XGB.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V24 minus strand signal of all reads GRCh38 94.1 MB link
ENCFF779PSE ENCFF779PSE.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V29 minus strand signal of all reads GRCh38 89.1 MB link
ENCFF866PLF ENCFF866PLF.bigWig bigWig (minus strand signal of all reads); assembly: GRCh38; genome annotation: V29 minus strand signal of all reads GRCh38 94.1 MB link
ENCFF014DGM ENCFF014DGM.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 92.4 MB link
ENCFF037OAP ENCFF037OAP.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 86.1 MB link
ENCFF134AUV ENCFF134AUV.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 81.7 MB link
ENCFF272HKN ENCFF272HKN.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 76.5 MB link
ENCFF584IBH ENCFF584IBH.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 81.3 MB link
ENCFF914EUS ENCFF914EUS.bigWig bigWig (minus strand signal of all reads); assembly: hg19; genome annotation: V19 minus strand signal of all reads hg19 88.4 MB link
ENCFF234YRX ENCFF234YRX.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 78.2 MB link
ENCFF327PGP ENCFF327PGP.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 73.7 MB link
ENCFF469EBA ENCFF469EBA.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 78.0 MB link
ENCFF812VFP ENCFF812VFP.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 minus strand signal of unique reads GRCh38 83.1 MB link
ENCFF046SYF ENCFF046SYF.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 minus strand signal of unique reads GRCh38 82.2 MB link
ENCFF299QHA ENCFF299QHA.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 minus strand signal of unique reads GRCh38 78.2 MB link
ENCFF166LCZ ENCFF166LCZ.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 70.7 MB link
ENCFF206OOZ ENCFF206OOZ.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 83.0 MB link
ENCFF549AQP ENCFF549AQP.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 77.5 MB link
ENCFF592BEG ENCFF592BEG.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 74.7 MB link
ENCFF606WUK ENCFF606WUK.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 79.0 MB link
ENCFF885JUQ ENCFF885JUQ.bigWig bigWig (minus strand signal of unique reads); assembly: hg19; genome annotation: V19 minus strand signal of unique reads hg19 73.7 MB link
ENCFF070OXC ENCFF070OXC.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 90.2 MB link
ENCFF477UQU ENCFF477UQU.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 84.8 MB link
ENCFF561OEM ENCFF561OEM.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 80.7 MB link
ENCFF615OHL ENCFF615OHL.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V24 plus strand signal of all reads GRCh38 95.3 MB link
ENCFF504FXZ ENCFF504FXZ.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V29 plus strand signal of all reads GRCh38 95.3 MB link
ENCFF750JSQ ENCFF750JSQ.bigWig bigWig (plus strand signal of all reads); assembly: GRCh38; genome annotation: V29 plus strand signal of all reads GRCh38 90.2 MB link
ENCFF125GEQ ENCFF125GEQ.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 82.8 MB link
ENCFF334JZI ENCFF334JZI.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 83.3 MB link
ENCFF362LAA ENCFF362LAA.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 93.7 MB link
ENCFF662LND ENCFF662LND.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 77.9 MB link
ENCFF691JRW ENCFF691JRW.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 89.6 MB link
ENCFF833OKT ENCFF833OKT.bigWig bigWig (plus strand signal of all reads); assembly: hg19; genome annotation: V19 plus strand signal of all reads hg19 87.6 MB link
ENCFF143ORL ENCFF143ORL.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 85.1 MB link
ENCFF317RWL ENCFF317RWL.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 80.1 MB link
ENCFF344JDU ENCFF344JDU.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 75.3 MB link
ENCFF854JTS ENCFF854JTS.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V24 plus strand signal of unique reads GRCh38 79.8 MB link
ENCFF084GGK ENCFF084GGK.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 plus strand signal of unique reads GRCh38 80.1 MB link
ENCFF830VBK ENCFF830VBK.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38; genome annotation: V29 plus strand signal of unique reads GRCh38 84.1 MB link
ENCFF005CIQ ENCFF005CIQ.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 75.6 MB link
ENCFF081AHZ ENCFF081AHZ.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 72.7 MB link
ENCFF198GLG ENCFF198GLG.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 79.5 MB link
ENCFF627LWK ENCFF627LWK.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 85.1 MB link
ENCFF795DIJ ENCFF795DIJ.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 81.1 MB link
ENCFF975UHW ENCFF975UHW.bigWig bigWig (plus strand signal of unique reads); assembly: hg19; genome annotation: V19 plus strand signal of unique reads hg19 76.8 MB link
ENCFF075JON ENCFF075JON.fastq fastq (reads) reads 2.5 GB link
ENCFF150HWI ENCFF150HWI.fastq fastq (reads) reads 2.3 GB link
ENCFF290TFQ ENCFF290TFQ.fastq fastq (reads) reads 2.2 GB link
ENCFF796EGU ENCFF796EGU.fastq fastq (reads) reads 2.4 GB link
ENCFF088OTT ENCFF088OTT.tar tar (differential splicing quantifications); assembly: hg19; genome annotation: V19 differential splicing quantifications hg19 3.4 MB link
ENCFF699TOM ENCFF699TOM.tar tar (differential splicing quantifications); assembly: hg19; genome annotation: V19 differential splicing quantifications hg19 3.9 MB link
ENCFF770UDB ENCFF770UDB.tar tar (differential splicing quantifications); assembly: hg19; genome annotation: V19 differential splicing quantifications hg19 14.9 MB link
ENCFF212CVT ENCFF212CVT.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 2.8 MB link
ENCFF242HIL ENCFF242HIL.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 5.5 MB link
ENCFF651POU ENCFF651POU.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 1.7 MB link
ENCFF770AIB ENCFF770AIB.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 4.1 MB link
ENCFF798KAI ENCFF798KAI.tsv tsv (differential expression quantifications); assembly: hg19; genome annotation: V19 differential expression quantifications hg19 2.0 MB link
ENCFF472TXR ENCFF472TXR.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V24 gene quantifications GRCh38 9.4 MB link
ENCFF928QMV ENCFF928QMV.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V24 gene quantifications GRCh38 9.4 MB link
ENCFF574BOB ENCFF574BOB.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V29 gene quantifications GRCh38 10.4 MB link
ENCFF687TRM ENCFF687TRM.tsv tsv (gene quantifications); assembly: GRCh38; genome annotation: V29 gene quantifications GRCh38 10.4 MB link
ENCFF383HNM ENCFF383HNM.tsv tsv (gene quantifications); assembly: hg19; genome annotation: V19 gene quantifications hg19 9.1 MB link
ENCFF426XLC ENCFF426XLC.tsv tsv (gene quantifications); assembly: hg19; genome annotation: V19 gene quantifications hg19 9.1 MB link
ENCFF336MTN ENCFF336MTN.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V24 transcript quantifications GRCh38 25.3 MB link
ENCFF945ZGY ENCFF945ZGY.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V24 transcript quantifications GRCh38 25.3 MB link
ENCFF013YLN ENCFF013YLN.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 29.8 MB link
ENCFF147PIU ENCFF147PIU.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 27.4 MB link
ENCFF894UJY ENCFF894UJY.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 29.8 MB link
ENCFF932XPP ENCFF932XPP.tsv tsv (transcript quantifications); assembly: GRCh38; genome annotation: V29 transcript quantifications GRCh38 27.3 MB link
ENCFF338UJR ENCFF338UJR.tsv tsv (transcript quantifications); assembly: hg19; genome annotation: V19 transcript quantifications hg19 24.9 MB link
ENCFF343ZNU ENCFF343ZNU.tsv tsv (transcript quantifications); assembly: hg19; genome annotation: V19 transcript quantifications hg19 24.9 MB link