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ENCSR539BEV

ENCSR ENCODE
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eCLIP experiment on HepG2 against UPF1

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

Relations

control:ENCSR042RCU

Summary

eCLIP of UPF1 in Homo sapiens HepG2

Overall Design

eCLIP experiment on HepG2 against UPF1

Analysis

View Data Processing
Analysis page is available for ENCSR539BEV.

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: 2.1 GB
Assay: eCLIP
Target: UPF1
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
ENCFF699EEF ENCFF699EEF.bam bam (alignments); assembly: GRCh38 alignments GRCh38 180.7 MB link
ENCFF811KHK ENCFF811KHK.bam bam (alignments); assembly: GRCh38 alignments GRCh38 246.1 MB link
ENCFF315BLR ENCFF315BLR.bam bam (alignments); assembly: hg19 alignments hg19 186.8 MB link
ENCFF787DWG ENCFF787DWG.bam bam (alignments); assembly: hg19 alignments hg19 253.9 MB link
ENCFF368XBY ENCFF368XBY.bed bed (peaks); assembly: GRCh38 peaks GRCh38 576.8 KB link
ENCFF687EQE ENCFF687EQE.bed bed (peaks); assembly: GRCh38 peaks GRCh38 225.7 KB link
ENCFF763ZLD ENCFF763ZLD.bed bed (peaks); assembly: GRCh38 peaks GRCh38 722.4 KB link
ENCFF242FDW ENCFF242FDW.bed bed (peaks); assembly: hg19 peaks hg19 222.8 KB link
ENCFF483STL ENCFF483STL.bed bed (peaks); assembly: hg19 peaks hg19 712.5 KB link
ENCFF848JHB ENCFF848JHB.bed bed (peaks); assembly: hg19 peaks hg19 578.3 KB link
ENCFF072RII ENCFF072RII.bigBed bigBed (peaks); assembly: GRCh38 peaks GRCh38 1.1 MB link
ENCFF218EGF ENCFF218EGF.bigBed bigBed (peaks); assembly: GRCh38 peaks GRCh38 1.4 MB link
ENCFF050BHJ ENCFF050BHJ.bigBed bigBed (peaks); assembly: hg19 peaks hg19 1.4 MB link
ENCFF517FAK ENCFF517FAK.bigBed bigBed (peaks); assembly: hg19 peaks hg19 1.2 MB link
ENCFF400GTE ENCFF400GTE.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38 minus strand signal of unique reads GRCh38 8.4 MB link
ENCFF429YRX ENCFF429YRX.bigWig bigWig (minus strand signal of unique reads); assembly: GRCh38 minus strand signal of unique reads GRCh38 11.3 MB link
ENCFF168ORJ ENCFF168ORJ.bigWig bigWig (minus strand signal of unique reads); assembly: hg19 minus strand signal of unique reads hg19 8.5 MB link
ENCFF992OTW ENCFF992OTW.bigWig bigWig (minus strand signal of unique reads); assembly: hg19 minus strand signal of unique reads hg19 11.5 MB link
ENCFF101ODP ENCFF101ODP.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38 plus strand signal of unique reads GRCh38 8.8 MB link
ENCFF998KED ENCFF998KED.bigWig bigWig (plus strand signal of unique reads); assembly: GRCh38 plus strand signal of unique reads GRCh38 11.8 MB link
ENCFF072CTB ENCFF072CTB.bigWig bigWig (plus strand signal of unique reads); assembly: hg19 plus strand signal of unique reads hg19 12.1 MB link
ENCFF153YEG ENCFF153YEG.bigWig bigWig (plus strand signal of unique reads); assembly: hg19 plus strand signal of unique reads hg19 8.9 MB link
ENCFF022DHH ENCFF022DHH.fastq fastq (reads) reads 295.8 MB link
ENCFF528BUU ENCFF528BUU.fastq fastq (reads) reads 312.7 MB link
ENCFF881UQQ ENCFF881UQQ.fastq fastq (reads) reads 287.2 MB link
ENCFF943HIX ENCFF943HIX.fastq fastq (reads) reads 316.7 MB link