RT Journal Article
SR Electronic
T1 Resources for the comprehensive discovery of functional RNA elements
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 030486
DO 10.1101/030486
A1 Balaji Sundararaman
A1 Lijun Zhan
A1 Steven Blue
A1 Rebecca Stanton
A1 Keri Elkins
A1 Sara Olson
A1 Xintao Wei
A1 Eric L. Van Nostrand
A1 Stephanie C. Huelga
A1 Brendan M. Smalec
A1 Xiaofeng Wang
A1 Eurie L. Hong
A1 Jean M. Davidson
A1 Eric Lecuyer
A1 Brenton R. Graveley
A1 Gene W. Yeo
YR 2015
UL http://biorxiv.org/content/early/2015/11/02/030486.abstract
AB Transcriptome-wide maps of RNA binding protein (RBP)-RNA interactions by immunoprecipitation (IP)-based methods such as RNA IP (RIP) and crosslinking and IP (CLIP) are key starting points for evaluating the molecular roles of the thousands of human RBPs. A significant bottleneck to the application of these methods in diverse cell-lines, tissues and developmental stages, is the availability of validated IP-quality antibodies. Using IP followed by immunoblot assays, we have developed a validated repository of 438 commercially available antibodies that interrogate 365 unique RBPs. In parallel, 362 short-hairpin RNA (shRNA) constructs against 276 unique RBPs were also used to confirm specificity of these antibodies. These antibodies can characterize subcellular RBP localization. With the burgeoning interest in the roles of RBPs in cancer, neurobiology and development, these resources are invaluable to the broad scientific community. Detailed information about these resources is publicly available at the ENCODE portal (https://www.encodeproject.org/).HighlightsAntibodies against 365 unique RBPs successfully immunoprecipitate the RBPsShort-hairpin RNAs against 276 unique RBPs confirm the specificity of RBP antibodiesAntibodies characterize subcellular localization of RBPsAntibody and hairpin RNA information are provided at https://www.encodeproject.org/