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

Miriam Schreiber; Jamie Orr; Abdellah Barakate; Robbie Waugh

doi:10.1007/978-1-0716-2253-7_20

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)

Plant Sciences

Research output: Chapter in Book/Report/Conference proceeding › Chapter

1 Citation (Scopus)

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 language	English
Title of host publication	Plant Gametogenesis
Subtitle of host publication	Methods and Protocols
Editors	Christophe Lambing
Place of Publication	New York
Publisher	Humana Press
Pages	291-311
Number of pages	21
Edition	1st
ISBN (Electronic)	9781071622537
ISBN (Print)	9781071622520
DOIs	https://doi.org/10.1007/978-1-0716-2253-7_20
Publication status	Published - 24 Apr 2022

Publication series

Name	Methods in Molecular Biology
Volume	2484
ISSN (Print)	1064-3745
ISSN (Electronic)	1940-6029

Keywords

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

ASJC Scopus subject areas

Molecular Biology
Genetics

Access to Document

10.1007/978-1-0716-2253-7_20

Cite this

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

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.",

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Barley (Hordeum Vulgare) Anther and Meiocyte RNA Sequencing: Mapping Sequencing Reads and Downstream Data Analyses. / Schreiber, Miriam; Orr, Jamie; Barakate, Abdellah et al.
Plant Gametogenesis: Methods and Protocols. ed. / Christophe Lambing. 1st. ed. New York: Humana Press, 2022. p. 291-311 (Methods in Molecular Biology; Vol. 2484).

Research output: Chapter in Book/Report/Conference proceeding › Chapter

TY - CHAP

T1 - Barley (Hordeum Vulgare) Anther and Meiocyte RNA Sequencing

T2 - Mapping Sequencing Reads and Downstream Data Analyses

AU - Schreiber, Miriam

AU - Orr, Jamie

AU - Barakate, Abdellah

AU - Waugh, Robbie

PY - 2022/4/24

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KW - 3D-RNA-seq

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KW - Differential gene expression

KW - Meiosis

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

Abstract

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Keywords

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