title: Resources for the Comprehensive Discovery of Functional RNA Elements.
abstract: 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/).
authors.affiliation: Department of Cellular and Molecular Medicine, Institute for Genomic Medicine, Stem Cell Program, Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA 92037, USA.
authors.forename: Balaji
authors.initials: B
authors.lastname: Sundararaman
authors.affiliation: Department of Genetics and Genome Sciences, Institute for Systems Genomics, UConn Health, Farmington, CT 06030, USA.
authors.forename: Lijun
authors.initials: L
authors.lastname: Zhan
authors.affiliation: Department of Cellular and Molecular Medicine, Institute for Genomic Medicine, Stem Cell Program, Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA 92037, USA.
authors.forename: Steven M
authors.initials: SM
authors.lastname: Blue
authors.affiliation: Department of Cellular and Molecular Medicine, Institute for Genomic Medicine, Stem Cell Program, Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA 92037, USA.
authors.forename: Rebecca
authors.initials: R
authors.lastname: Stanton
authors.affiliation: Department of Cellular and Molecular Medicine, Institute for Genomic Medicine, Stem Cell Program, Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA 92037, USA.
authors.forename: Keri
authors.initials: K
authors.lastname: Elkins
authors.affiliation: Department of Genetics and Genome Sciences, Institute for Systems Genomics, UConn Health, Farmington, CT 06030, USA.
authors.forename: Sara
authors.initials: S
authors.lastname: Olson
authors.affiliation: Department of Genetics and Genome Sciences, Institute for Systems Genomics, UConn Health, Farmington, CT 06030, USA.
authors.forename: Xintao
authors.initials: X
authors.lastname: Wei
authors.affiliation: Department of Cellular and Molecular Medicine, Institute for Genomic Medicine, Stem Cell Program, Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA 92037, USA.
authors.forename: Eric L
authors.initials: EL
authors.lastname: Van Nostrand
authors.affiliation: Department of Cellular and Molecular Medicine, Institute for Genomic Medicine, Stem Cell Program, Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA 92037, USA.
authors.forename: Gabriel A
authors.initials: GA
authors.lastname: Pratt
authors.affiliation: Department of Cellular and Molecular Medicine, Institute for Genomic Medicine, Stem Cell Program, Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA 92037, USA.
authors.forename: Stephanie C
authors.initials: SC
authors.lastname: Huelga
authors.affiliation: Department of Genetics and Genome Sciences, Institute for Systems Genomics, UConn Health, Farmington, CT 06030, USA.
authors.forename: Brendan M
authors.initials: BM
authors.lastname: Smalec
authors.affiliation: Département de Biochimie, Université de Montréal; Division of Experimental Medicine, McGill University; Institut de Recherches Cliniques de Montréal (IRCM), Montréal, QC H2W 1R7, Canada.
authors.forename: Xiaofeng
authors.initials: X
authors.lastname: Wang
authors.affiliation: ENCODE Data Coordinating Center (DCC), Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA.
authors.forename: Eurie L
authors.initials: EL
authors.lastname: Hong
authors.affiliation: ENCODE Data Coordinating Center (DCC), Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA.
authors.forename: Jean M
authors.initials: JM
authors.lastname: Davidson
authors.affiliation: Département de Biochimie, Université de Montréal; Division of Experimental Medicine, McGill University; Institut de Recherches Cliniques de Montréal (IRCM), Montréal, QC H2W 1R7, Canada.
authors.forename: Eric
authors.initials: E
authors.lastname: Lécuyer
authors.affiliation: Department of Genetics and Genome Sciences, Institute for Systems Genomics, UConn Health, Farmington, CT 06030, USA. Electronic address: graveley@uchc.edu.
authors.forename: Brenton R
authors.initials: BR
authors.lastname: Graveley
authors.affiliation: Department of Cellular and Molecular Medicine, Institute for Genomic Medicine, Stem Cell Program, Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA 92037, USA. Electronic address: geneyeo@ucsd.edu.
authors.forename: Gene W
authors.initials: GW
authors.lastname: Yeo
mesh_terms: D001665:Binding Sites; D030541:Databases, Genetic; D006801:Humans; D011485:Protein Binding; D012313:RNA / Q000235:genetics / Q000378:metabolism*; D034741:RNA, Small Interfering / Q000145:classification / Q000235:genetics; D016601:RNA-Binding Proteins / Q000235:genetics* / Q000378:metabolism; D059467:Transcriptome / Q000235:genetics*
chemical_list: D034741:RNA, Small Interfering; D016601:RNA-Binding Proteins; D012313:RNA