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. 2023:2704:99-113.
doi: 10.1007/978-1-0716-3385-4_6.

RNA Preparation and RNA-Seq Bioinformatics for Comparative Transcriptomics

Antonio Rodríguez-García  1   2 , Alberto Sola-Landa  3   4 , Carlos Barreiro  3   5
Affiliations

RNA Preparation and RNA-Seq Bioinformatics for Comparative Transcriptomics

Antonio Rodríguez-García et al. Methods Mol Biol. 2023.

Abstract

The principal transcriptome analysis is the determination of differentially expressed genes across experimental conditions. For this, the next-generation sequencing of RNA (RNA-seq) has several advantages over other techniques, such as the capability of detecting all the transcripts in one assay over RT-qPCR, such as its higher accuracy and broader dynamic range over microarrays or the ability to detect novel transcripts, including non-coding RNA molecules, at nucleotide-level resolution over both techniques. Despite these advantages, many microbiology laboratories have not yet applied RNA-seq analyses to their investigations. The high cost of the equipment for next-generation sequencing is no longer an issue since this intermediate part of the analysis can be provided by commercial or central services. Here, we detail a protocol for the first part of the analysis, the RNA extraction and an introductory protocol to the bioinformatics analysis of the sequencing data to generate the differential expression results.

Keywords: Bioconductor; Differential expression; RNA extraction; RNA-seq; Transcriptomics.

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