Barley (Hordeum Vulgare) Anther and Meiocyte RNA Sequencing: Mapping Sequencing Reads and Downstream Data Analyses

Miriam Schreiber, Jamie Orr, Abdellah Barakate, Robbie Waugh (Lead / Corresponding author)

Research output: Chapter in Book/Report/Conference proceedingChapter

Abstract

RNA sequencing (RNA-seq) data is by now the most common method to study differential gene expression. Here we present a pipeline from RNA-seq generation to analysis with examples based on our own barley anther and meiocyte transcriptome. The bioinformatics pipeline will give everyone, from a beginner to a more experienced user, the possibility to analyze their datasets and identify significantly differentially expressed genes. It also allows differential alternative splicing analysis which will become increasingly common due to the high regulatory impact on the gene expression. We describe use of the Galaxy interface for RNA-seq read quantification and the 3D RNA-seq app for the downstream data analysis.

Original languageEnglish
Title of host publicationPlant Gametogenesis
Subtitle of host publicationMethods and Protocols
EditorsChristophe Lambing
Place of PublicationNew York
PublisherHumana Press Inc.
Pages291-311
Number of pages21
Edition1st
ISBN (Electronic)9781071622537
ISBN (Print)9781071622520
DOIs
Publication statusPublished - 24 Apr 2022

Publication series

NameMethods in Molecular Biology
Volume2484
ISSN (Print)1064-3745
ISSN (Electronic)1940-6029

Keywords

  • 3D-RNA-seq
  • Alternative splicing
  • Barley
  • Differential gene expression
  • Meiosis
  • RNA sequencing

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