GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Series GSE15769 Query DataSets for GSE15769
Status Public on Jun 07, 2009
Title RNAcompete: a method for rapid and systematic analysis of the RNA recognition specificities of RNA-binding proteins
Organism synthetic construct
Experiment type Other
Summary Metazoan genomes encode hundreds of RNA binding proteins (RBPs) but relatively few have well-defined RNA-binding preferences. Current techniques for determining RNA targets, including those involving in vitro selection and RNA co-immunoprecipitation, require significant time and labour investment. Here we introduce RNAcompete, a new method for the systematic analysis of RNA-binding specificities that employs a single binding reaction to determine the relative preferences of RBPs for short RNAs that containing a complete range of k-mers in structured and unstructured RNA contexts. We tested RNAcompete by analyzing nine diverse RBPs (HuR, Vts1, FUSIP1, PTB, U1A, SF2/ASF, SLM2, RBM4, and YB1). RNAcompete identified both expected and previously unknown RNA binding preferences. Using in vitro and in vivo binding data, we demonstrate that preferences for individual 7-mers identified by RNAcompete are a more accurate representation of binding activity than conventional motif models. We anticipate that RNAcompete will be a valuable tool for the large-scale study of RNA-protein interactions.
Overall design The bound RNA from each RNA binding protein pulldown assay is analyzed on a custom Agilent microarray using a pool RNA control as a reference.
Web link
Contributor(s) Ray D, Kazan H, Chan ET, Pena-Castillo L, Chaudhry S, Talukder S, Blencowe BJ, Morris QD, Hughes TR
Citation(s) 19561594
Submission date Apr 21, 2009
Last update date Mar 21, 2012
Contact name Esther T Chan
Organization name Celgene Corporation
Street address 1500 Owens Street, Suite 500
City San Francisco
State/province California
ZIP/Postal code 94158
Country USA
Platforms (1)
GPL8464 Agilent custom 244K oligo RNA Binding Protein microarray v2
Samples (10)
GSM395747 Fusip1 pulldown experiment
GSM395748 GST pulldown experiment
GSM395749 HuR pulldown experiment
BioProject PRJNA116807

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
GSE15769_RAW.tar 68.0 Mb (http)(custom) TAR (of TXT)
Processed data included within Sample table

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