Zambelli Federico, Pavesi Giulio
Dipartimento di Bioscienze, Università di Milano, Via Celoria 26, 20133, Milano, Italy.
Methods Mol Biol. 2015;1269:293-303. doi: 10.1007/978-1-4939-2291-8_18.
Next-generation sequencing (NGS) technologies have opened new avenues of unprecedented power for research in molecular biology and genetics. In particular, their application to the study of RNA-binding proteins (RBPs), extracted through immunoprecipitation (RIP), permits to sequence and characterize all RNAs that were found to be bound in vivo by a given RBP (RIP-Seq). On the other hand, NGS-based experiments, including RIP-Seq, produce millions of short sequence fragments that have to be processed with suitable bioinformatic tools and methods to recover and/or quantify the original sequence sample. In this chapter we provide a survey of different approaches that can be taken for the analysis of RIP-Seq data and the identification of the RNAs bound by a given RBP.
新一代测序（NGS）技术为分子生物学和遗传学研究开辟了前所未有的强大新途径。特别是，将其应用于通过免疫沉淀（RIP）提取的RNA结合蛋白（RBP）的研究中，能够对给定RBP在体内结合的所有RNA进行测序和表征（RIP-Seq）。另一方面，基于NGS的实验，包括RIP-Seq，会产生数百万个短序列片段，必须使用合适的生物信息学工具和方法进行处理，以恢复和/或定量原始序列样本。在本章中，我们将概述可用于分析RIP-Seq数据以及鉴定给定RBP结合的RNA的不同方法。
