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ENCSR040QLV

ENCSR ENCODE
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eCLIP experiment on K562 against DDX21

Organism: Homo sapiens
Experiment Types:
eCLIP
Status: released
Contact: Gene Yeo, UCSD

Relations

control:ENCSR266XXD

Summary

eCLIP of DDX21 in Homo sapiens K562

Overall Design

eCLIP experiment on K562 against DDX21

Analysis

View Data Processing
Analysis page is available for ENCSR040QLV.

Dataset Citations (2)

Principles of RNA processing from analysis of enhanced CLIP maps for 150 RNA binding proteins.
PMID 32252787 · 2020 · Genome biology
Eric L Van Nostrand, Gabriel A Pratt, Brian A Yee, Emily C Wheeler, Steven M Blue, Jasmine Mueller, Samuel S Park, Keri E Garcia, Chelsea Gelboin-Burkhart, Thai B Nguyen, Ines Rabano, Rebecca Stanton, Balaji Sundararaman, Ruth Wang, Xiang-Dong Fu, Brenton R Graveley, Gene W Yeo
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: 3.3 GB
Assay: eCLIP
Target: DDX21
Biosample: Homo sapiens K562
Files: 26
Unique ENC file IDs: 26
File Formats
bigWig (8) bed (6) bam (4) bigBed (4) fastq (4)
Output types (5)
peaks (10) alignments (4) minus strand signal of unique reads (4) plus strand signal of unique reads (4) reads (4)

Linked Publications (2)

Principles of RNA processing from analysis of enhanced CLIP maps for 150 RNA binding proteins.
Genome biology · 2020
A large-scale binding and functional map of human RNA-binding proteins.
Nature · 2020

Data Files (26)

Accession File Name Stored Type Output Type Mapping Assembly Size Download
ENCFF455REV ENCFF455REV.bam bam (alignments); assembly: GRCh38 alignments GRCh38 166.1 MB link
ENCFF655QSG ENCFF655QSG.bam bam (alignments); assembly: GRCh38 alignments GRCh38 85.9 MB link
ENCFF099RYM ENCFF099RYM.bam bam (alignments); assembly: hg19 alignments hg19 88.2 MB link
ENCFF845KUG ENCFF845KUG.bam bam (alignments); assembly: hg19 alignments hg19 169.9 MB link
ENCFF005ZCI ENCFF005ZCI.bed bed (peaks); assembly: GRCh38 peaks GRCh38 356.2 KB link
ENCFF371SNO ENCFF371SNO.bed bed (peaks); assembly: GRCh38 peaks GRCh38 746.4 KB link
ENCFF378OYA ENCFF378OYA.bed bed (peaks); assembly: GRCh38 peaks GRCh38 2.1 KB link
ENCFF572GMO ENCFF572GMO.bed bed (peaks); assembly: hg19 peaks hg19 364.3 KB link
ENCFF800GPC ENCFF800GPC.bed bed (peaks); assembly: hg19 peaks hg19 2.2 KB link
ENCFF945XNS ENCFF945XNS.bed bed (peaks); assembly: hg19 peaks hg19 747.9 KB link
ENCFF028CQB ENCFF028CQB.bigBed bigBed (peaks); assembly: GRCh38 peaks GRCh38 753.8 KB link
ENCFF159PUC ENCFF159PUC.bigBed bigBed (peaks); assembly: GRCh38 peaks GRCh38 1.3 MB link
ENCFF420HTZ ENCFF420HTZ.bigBed bigBed (peaks); assembly: hg19 peaks hg19 1.3 MB link
ENCFF559UQP ENCFF559UQP.bigBed bigBed (peaks); assembly: hg19 peaks hg19 769.4 KB link
ENCFF006QTI ENCFF006QTI.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38 minus strand signal of unique reads GRCh38 10.3 MB link
ENCFF485TSN ENCFF485TSN.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38 minus strand signal of unique reads GRCh38 5.3 MB link
ENCFF180UZN ENCFF180UZN.bigWig bigWig (minus strand signal of unique reads); assembly: hg19 minus strand signal of unique reads hg19 10.4 MB link
ENCFF353WIB ENCFF353WIB.bigWig bigWig (minus strand signal of unique reads); assembly: hg19 minus strand signal of unique reads hg19 5.3 MB link
ENCFF139OJJ ENCFF139OJJ.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38 plus strand signal of unique reads GRCh38 5.5 MB link
ENCFF402AXI ENCFF402AXI.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38 plus strand signal of unique reads GRCh38 10.8 MB link
ENCFF429PEL ENCFF429PEL.bigWig bigWig (plus strand signal of unique reads); assembly: hg19 plus strand signal of unique reads hg19 5.6 MB link
ENCFF740MPP ENCFF740MPP.bigWig bigWig (plus strand signal of unique reads); assembly: hg19 plus strand signal of unique reads hg19 11.0 MB link
ENCFF253EGX ENCFF253EGX.fastq fastq (reads) reads 729.6 MB link
ENCFF363TSA ENCFF363TSA.fastq fastq (reads) reads 700.8 MB link
ENCFF671GCD ENCFF671GCD.fastq fastq (reads) reads 666.0 MB link
ENCFF946SJB ENCFF946SJB.fastq fastq (reads) reads 681.5 MB link