Analysis of ROS-Triggered Changes in the Transcriptome

Patrick Willems

doi:10.1007/978-1-0716-2469-2_20

Analysis of ROS-Triggered Changes in the Transcriptome

Methods Mol Biol. 2022:2526:277-288. doi: 10.1007/978-1-0716-2469-2_20.

Author

Patrick Willems^{1

2}

Affiliations

¹ Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium. pawil@psb.ugent.be.
² Center for Plant Systems Biology, VIB, Ghent, Belgium. pawil@psb.ugent.be.

PMID: 35657527
DOI: 10.1007/978-1-0716-2469-2_20

Abstract

RNA sequencing is routinely used for determining transcriptome-wide expression changes during various conditions, including oxidative stress conditions. In this chapter, a basic workflow to determine differentially expressed genes between two conditions of interest is provided. After providing brief guidelines for experimental design, we provide step-by-step instructions for genome alignment of reads and differential expression analysis.

Keywords: Differential gene expression; Genome alignment; Next-generation sequencing; Reactive oxygen species; Transcriptomics; edgeR; mRNA-sequencing.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Gene Expression Profiling*
Genome
High-Throughput Nucleotide Sequencing
Reactive Oxygen Species / metabolism
Sequence Analysis, RNA
Transcriptome*

Substances

Reactive Oxygen Species