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. 2022:2418:405-424.
doi: 10.1007/978-1-0716-1920-9_22.

RNA-Seq Experiment and Data Analysis

Miyuraj Harishchandra Hikkaduwa Withanage  1 , Hanquan Liang  2 , Erliang Zeng  3   4   5   6
Affiliations

RNA-Seq Experiment and Data Analysis

Miyuraj Harishchandra Hikkaduwa Withanage et al. Methods Mol Biol. 2022.

Abstract

With the ability to obtain several millions of reads per sample, high-throughput RNA sequencing (RNA-Seq) enables investigation of any transcriptome at a fine resolution. Not just the messenger RNA (mRNA), but a wide variety of different RNA populations (e.g., total RNA, microRNA, long ncRNA, pre-mRNA) can also be investigated using RNA-Seq. While facilitating accurate quantification of gene expression, RNA-Seq offers the opportunity to estimate abundance of isoforms and find novel transcripts and allele-specific transcripts. In this chapter, we describe a protocol to construct an RNA-Seq library for sequencing on Illumina NGS platforms and a computational pipeline to perform RNA-Seq data analysis. The protocols described in this chapter can be applied to the analysis of differential gene expression in control versus 17β-estradiol treatment of in vivo or in vitro systems.

Keywords: Bioconductor; Data analysis; Differentially expressed genes; Next-generation sequencing; RNA-Seq; Statistical analysis.

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