GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Series GSE28864 Query DataSets for GSE28864
Status Public on May 15, 2011
Title A quantitative analysis of CLIP methods for identifying binding sites of RNA-binding proteins (mRNA-seq)
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Crosslinking and immunoprecipitation (CLIP) is increasingly used to map transcriptome-wide binding sites of RNA-binding proteins (RBPs). We developed a method for CLIP data analysis and applied it to compare 254 nm CLIP with PAR-CLIP, which involves crosslinking of photoreactive nucleotides with 365 nm UV light. We found small differences in the accuracy of these methods in identifying binding sites of HuR, a protein that binds low-complexity sequences and Argonaute 2, which has a complex binding specificity. We show that crosslink-induced mutations lead to single-nucleotide resolution for both PAR-CLIP and CLIP. Our results confirm the expectation from original CLIP publications that RNA-binding proteins do not protect sufficiently their sites under the denaturing conditions used during the CLIP procedure, and we show that extensive digestion with sequence-specific ribonucleases strongly biases the set of recovered binding sites. We finally show that this bias can be substantially reduced by milder nuclease digestion conditions.
Overall design We performed duplicate mRNA-Seq experiments for cells grown in the presence of modified nucleotides or in normal medium, and following crosslinking at 365nm, 254nm or without crosslinking. In addition, we performed single mRNA-Seq experiments of cells transfected with anti-GFP or anti-HuR siRNA.
Contributor(s) Kishore S, Jaskiewicz L, Burger L, Hausser J, Khorshid M, Zavolan M
Citation(s) 21572407
Submission date Apr 26, 2011
Last update date May 15, 2019
Contact name Jean Hausser
Organization name Weizmann Institute of Science
Street address Herzl St.
City Rehovot
ZIP/Postal code 76100
Country Israel
Platforms (1)
GPL10999 Illumina Genome Analyzer IIx (Homo sapiens)
Samples (10)
GSM714678 mRNA-Seq_4SU_365XL_repA
GSM714679 mRNA-Seq_4SU_365XL_repB
GSM714680 mRNA-Seq_4SU_NOXL_repA
This SubSeries is part of SuperSeries:
GSE28865 A quantitative analysis of CLIP methods for identifying binding sites of RNA-binding proteins
SRA SRP006475
BioProject PRJNA153961

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
GSE28864_RAW.tar 3.2 Mb (http)(custom) TAR (of TAB)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap