CNR Institute of Biosciences and Bioresources, Research Division Portici, Portici, Italy.
Department of Agricultural Sciences, University of Naples "Federico II", Portici, Italy.
Methods Mol Biol. 2024;2832:67-79. doi: 10.1007/978-1-0716-3973-3_5.
Alternative splicing (AS) is an important mechanism contributing to stress-induced regulation of gene expression and proteome diversity. Massive sequencing technologies allow the identification of transcripts generated via stress-responsive AS, potentially important for adaptation to stress conditions. Several bioinformatics tools have been developed to identify differentially expressed alternative splicing events/transcripts from RNA-sequencing results. This chapter describes a detailed protocol for differential alternative splicing analysis using the rMATS tool. In addition, we provide guidelines for validation of the detected splice variants by qRT-PCR based on the obtained output files.
可变剪接（AS）是一种重要的机制，有助于应激诱导的基因表达和蛋白质组多样性的调节。大规模测序技术允许鉴定通过应激反应性 AS 产生的转录本，这些转录本可能对适应应激条件很重要。已经开发了几种生物信息学工具，用于从 RNA-seq 结果中鉴定差异表达的可变剪接事件/转录本。本章描述了使用 rMATS 工具进行差异可变剪接分析的详细方案。此外，我们还根据获得的输出文件，提供了基于 qRT-PCR 验证检测到的剪接变体的指南。
