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Series GSE77339 Query DataSets for GSE77339
Status Public on Mar 28, 2016
Title Enhanced CLIP (eCLIP) enables robust and scalable transcriptome-wide discovery and characterization of RNA binding protein binding sites [array]
Organism Homo sapiens
Experiment type Expression profiling by array
Summary RNA binding proteins (RBPs) play essential roles in cellular physiology by interacting with target RNAs. As defects in protein-RNA recognition lead to human disease, UV-crosslinking and immunoprecipitation (CLIP) of ribonuclear complexes followed by deep sequencing (-seq) is critical in constructing protein-RNA maps to expand our understanding of RBP function. However, current CLIP protocols are technically demanding and involve low complexity libraries that yield squandered sequencing of PCR duplicates and high experimental failure rates. To enable truly large-scale implementation of CLIP-seq, we have developed an enhanced CLIP methodology (eCLIP) that features a decrease of ~10 cycles of requisite amplification with a concomitant >60% decrease in discarded PCR duplicate reads, while maintaining the ability to identify RNA binding with single-nucleotide resolution. By simplifying the generation of paired IgG and size-matched input controls, eCLIP also dramatically improves specificity in discovery of authentic binding sites. To demonstrate that eCLIP enables large-scale and robust profiling of RBPs, 102 eCLIP experiments in biological duplicate for a diverse collection of 74 RBPs in HepG2 and K562 cells were completed (available at https://www.encodeproject.org). We establish that eCLIP is comparable in amplification and sample requirements to ChIP-seq, and enables integrative analysis of diverse RBPs to reveal factor-specific profiles, common artifacts for CLIP experiments and RNA-centric perspectives of RBP activity.
 
Overall design Microarray profiling of RBFOX2 knockdown by shRNAs in 293T cells
 
Contributor(s) Van Nostrand E, Pratt GA, Shishkin A, Gelboin-Burkhart C, Fang M, Sundararaman B, Blue S, Nguyen T, Surka C, Elkins K, Stanton R, Rigo F, Guttman M, Yeo G
Citation(s) 27018577
Submission date Jan 28, 2016
Last update date Jun 27, 2016
Contact name Gene Yeo
E-mail(s) geneyeo@ucsd.edu
Organization name UCSD
Street address 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab
City La Jolla
State/province CA
ZIP/Postal code 92037
Country USA
 
Platforms (1)
GPL17585 [HTA-2_0] Affymetrix Human Transcriptome Array 2.0 [probe set (exon) version]
Samples (12)
GSM2049426 Non-target control Rep1
GSM2049427 Non-target control Rep2
GSM2049428 Non-target control Rep3
This SubSeries is part of SuperSeries:
GSE77634 Enhanced CLIP (eCLIP) enables robust and scalable transcriptome-wide discovery and characterization of RNA binding protein binding sites
Relations
BioProject PRJNA310093

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE77339_RAW.tar 320.9 Mb (http)(custom) TAR (of CEL)
Processed data included within Sample table

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