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ENCSR735HOK

ENCSR ENCODE
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eCLIP experiment on HepG2 against YBX3

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

Relations

control:ENCSR700UGT

Summary

eCLIP of YBX3 in Homo sapiens HepG2

Overall Design

eCLIP experiment on HepG2 against YBX3

Analysis

View Data Processing
Analysis page is available for ENCSR735HOK.

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: 7.4 GB
Assay: eCLIP
Target: YBX3
Biosample: Homo sapiens HepG2
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
ENCFF148DUH ENCFF148DUH.bam bam (alignments); assembly: GRCh38 alignments GRCh38 708.2 MB link
ENCFF560ZTA ENCFF560ZTA.bam bam (alignments); assembly: GRCh38 alignments GRCh38 967.0 MB link
ENCFF331WIZ ENCFF331WIZ.bam bam (alignments); assembly: hg19 alignments hg19 1019.5 MB link
ENCFF843MHP ENCFF843MHP.bam bam (alignments); assembly: hg19 alignments hg19 732.1 MB link
ENCFF185OEI ENCFF185OEI.bed bed (peaks); assembly: GRCh38 peaks GRCh38 47.6 KB link
ENCFF311PHS ENCFF311PHS.bed bed (peaks); assembly: GRCh38 peaks GRCh38 1.4 MB link
ENCFF401TWM ENCFF401TWM.bed bed (peaks); assembly: GRCh38 peaks GRCh38 1.6 MB link
ENCFF075TIW ENCFF075TIW.bed bed (peaks); assembly: hg19 peaks hg19 49.0 KB link
ENCFF268SII ENCFF268SII.bed bed (peaks); assembly: hg19 peaks hg19 1.4 MB link
ENCFF904UKX ENCFF904UKX.bed bed (peaks); assembly: hg19 peaks hg19 1.4 MB link
ENCFF165UCU ENCFF165UCU.bigBed bigBed (peaks); assembly: GRCh38 peaks GRCh38 2.6 MB link
ENCFF570XZG ENCFF570XZG.bigBed bigBed (peaks); assembly: GRCh38 peaks GRCh38 3.1 MB link
ENCFF124VAO ENCFF124VAO.bigBed bigBed (peaks); assembly: hg19 peaks hg19 2.7 MB link
ENCFF668DJX ENCFF668DJX.bigBed bigBed (peaks); assembly: hg19 peaks hg19 2.7 MB link
ENCFF730NOU ENCFF730NOU.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38 minus strand signal of unique reads GRCh38 22.6 MB link
ENCFF988EAZ ENCFF988EAZ.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38 minus strand signal of unique reads GRCh38 26.3 MB link
ENCFF662AZS ENCFF662AZS.bigWig bigWig (minus strand signal of unique reads); assembly: hg19 minus strand signal of unique reads hg19 23.1 MB link
ENCFF781YNK ENCFF781YNK.bigWig bigWig (minus strand signal of unique reads); assembly: hg19 minus strand signal of unique reads hg19 27.2 MB link
ENCFF018RDR ENCFF018RDR.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38 plus strand signal of unique reads GRCh38 23.3 MB link
ENCFF771LAD ENCFF771LAD.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38 plus strand signal of unique reads GRCh38 26.9 MB link
ENCFF827BCE ENCFF827BCE.bigWig bigWig (plus strand signal of unique reads); assembly: hg19 plus strand signal of unique reads hg19 23.8 MB link
ENCFF893OBI ENCFF893OBI.bigWig bigWig (plus strand signal of unique reads); assembly: hg19 plus strand signal of unique reads hg19 27.8 MB link
ENCFF070GQY ENCFF070GQY.fastq fastq (reads) reads 830.2 MB link
ENCFF428UJW ENCFF428UJW.fastq fastq (reads) reads 960.0 MB link
ENCFF593QXS ENCFF593QXS.fastq fastq (reads) reads 983.7 MB link
ENCFF594XZD ENCFF594XZD.fastq fastq (reads) reads 1.1 GB link