Protocol to process crosslinking and immunoprecipitation data into annotated binding sites

Shuhao Xu; Grady G. Nguyen; Jack T. Naritomi; Hema M. Kopalle; Brian A. Yee; Katherine L. Rothamel; Evan A. Boyle; Gene W. Yeo

STAR Protocols (Jun 2024)

Protocol to process crosslinking and immunoprecipitation data into annotated binding sites

Shuhao Xu,
Grady G. Nguyen,
Jack T. Naritomi,
Hema M. Kopalle,
Brian A. Yee,
Katherine L. Rothamel,
Evan A. Boyle,
Gene W. Yeo

Affiliations

Shuhao Xu: Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92037, USA; Sanford Stem Cell Institute and Stem Cell Program, University of California, San Diego, La Jolla, CA 92037, USA; Institute for Genomic Medicine, UCSD Stem Cell Program, University of California, San Diego, La Jolla, CA 92037, USA
Grady G. Nguyen: Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92037, USA; Sanford Stem Cell Institute and Stem Cell Program, University of California, San Diego, La Jolla, CA 92037, USA; Institute for Genomic Medicine, UCSD Stem Cell Program, University of California, San Diego, La Jolla, CA 92037, USA
Jack T. Naritomi: Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92037, USA; Sanford Stem Cell Institute and Stem Cell Program, University of California, San Diego, La Jolla, CA 92037, USA; Institute for Genomic Medicine, UCSD Stem Cell Program, University of California, San Diego, La Jolla, CA 92037, USA
Hema M. Kopalle: Sanford Stem Cell Institute and Stem Cell Program, University of California, San Diego, La Jolla, CA 92037, USA; Institute for Genomic Medicine, UCSD Stem Cell Program, University of California, San Diego, La Jolla, CA 92037, USA; Department of Biological Sciences, University of California, San Diego, La Jolla, CA 92037, USA
Brian A. Yee: Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92037, USA; Sanford Stem Cell Institute and Stem Cell Program, University of California, San Diego, La Jolla, CA 92037, USA; Institute for Genomic Medicine, UCSD Stem Cell Program, University of California, San Diego, La Jolla, CA 92037, USA
Katherine L. Rothamel: Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92037, USA; Sanford Stem Cell Institute and Stem Cell Program, University of California, San Diego, La Jolla, CA 92037, USA; Institute for Genomic Medicine, UCSD Stem Cell Program, University of California, San Diego, La Jolla, CA 92037, USA; Center for RNA Technologies and Therapeutics, UC San Diego, La Jolla, CA 92037, USA
Evan A. Boyle: Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92037, USA
Gene W. Yeo: Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92037, USA; Sanford Stem Cell Institute and Stem Cell Program, University of California, San Diego, La Jolla, CA 92037, USA; Institute for Genomic Medicine, UCSD Stem Cell Program, University of California, San Diego, La Jolla, CA 92037, USA; Center for RNA Technologies and Therapeutics, UC San Diego, La Jolla, CA 92037, USA; Sanford Laboratories for Innovative Medicines, La Jolla, CA 92037, USA; Corresponding author

Journal volume & issue: Vol. 5, no. 2
p. 103040

Abstract

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Summary: Here, we present a protocol for using Skipper, a pipeline designed to process crosslinking and immunoprecipitation (CLIP) data into annotated binding sites. We describe steps for partitioning annotated transcript regions and fitting data to a beta-binomial model to call windows of enriched binding. From raw CLIP data, we detail how users can map reproducible RNA-binding sites to call enriched windows and perform downstream analysis. This protocol supports optional customizations for different use cases.For complete details on the use and execution of this protocol, please refer to Boyle et al.1 : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.

Published in STAR Protocols

ISSN: 2666-1667 (Online)
Publisher: Elsevier
Country of publisher: United States
LCC subjects: Science: Science (General)
Website: https://star-protocols.cell.com/

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