Barley (Hordeum Vulgare) Anther and Meiocyte RNA Sequencing: Mapping Sequencing Reads and Downstream Data Analyses.
3D-RNA-seq
Alternative splicing
Barley
Differential gene expression
Meiosis
RNA sequencing
Journal
Methods in molecular biology (Clifton, N.J.)
ISSN: 1940-6029
Titre abrégé: Methods Mol Biol
Pays: United States
ID NLM: 9214969
Informations de publication
Date de publication:
2022
2022
Historique:
entrez:
24
4
2022
pubmed:
25
4
2022
medline:
27
4
2022
Statut:
ppublish
Résumé
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.
Identifiants
pubmed: 35461459
doi: 10.1007/978-1-0716-2253-7_20
doi:
Substances chimiques
RNA
63231-63-0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
291-311Informations de copyright
© 2022. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.
Références
Geniza M, Jaiswal P (2017) Tools for building de novo transcriptome assembly. Curr Plant Biol 11-12:41–45
doi: 10.1016/j.cpb.2017.12.004
Hölzer M, Marz M (2019) De novo transcriptome assembly: a comprehensive cross-species comparison of short-read RNA-Seq assemblers. GigaScience 8(5):giz039
doi: 10.1093/gigascience/giz039
Lamarre S, Frasse P, Zouine M et al (2018) Optimization of an RNA-Seq differential gene expression analysis depending on biological replicate number and library size. Front Plant Sci 9:108
doi: 10.3389/fpls.2018.00108
Clark S, Yu F, Gu L et al (2019) Expanding alternative splicing identification by integrating multiple sources of transcription data in tomato. Front Plant Sci 10:689
doi: 10.3389/fpls.2019.00689
Zhang R, Calixto CPG, Marquez Y et al (2017) A high quality Arabidopsis transcriptome for accurate transcript-level analysis of alternative splicing. Nucleic Acids Res 45(9):5061–5073
doi: 10.1093/nar/gkx267
Barakate A, Orr J, Schreiber M et al (2021) Barley anther and Meiocyte transcriptome dynamics in meiotic prophase I. Front Plant Sci 11:619404
doi: 10.3389/fpls.2020.619404
Leinonen R, Sugawara H, Shumway M et al (2011) The sequence read archive. Nucleic Acids Res 39(Database issue):D19–D21
doi: 10.1093/nar/gkq1019
Afgan E, Baker D, Batut B et al (2018) The galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update. Nucleic Acids Res 46(W1):W537–W544
doi: 10.1093/nar/gky379
Guo W, Tzioutziou NA, Stephen G et al (2020) 3D RNA-seq: a powerful and flexible tool for rapid and accurate differential expression and alternative splicing analysis of RNA-seq data for biologists. RNA Biol 18(11):1574–1587
Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30(15):2114–2120
doi: 10.1093/bioinformatics/btu170
Patro R, Duggal G, Love MI et al (2017) Salmon provides fast and bias-aware quantification of transcript expression. Nat Methods 14(4):417–419
doi: 10.1038/nmeth.4197
Srivastava A, Malik L, Smith T et al (2019) Alevin efficiently estimates accurate gene abundances from dscRNA-seq data. Genome Biol 20(1):65
doi: 10.1186/s13059-019-1670-y
R Core Team. (2020) R: a language and environment for statistical computing. https://www.R-project.org/
Robinson MD, McCarthy DJ, Smyth GK (2010) edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26(1):139–140
doi: 10.1093/bioinformatics/btp616
Risso D, Ngai J, Speed TP et al (2014) Normalization of RNA-seq data using factor analysis of control genes or samples. Nat Biotechnol 32(9):896–902
doi: 10.1038/nbt.2931
Ritchie ME, Phipson B, Wu D et al (2015) Limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res 43(7):e47
doi: 10.1093/nar/gkv007
Guo W, Calixto CPG, Brown JWS et al (2017) TSIS: an R package to infer alternative splicing isoform switches for time-series data. Bioinformatics 33(20):3308–3310
doi: 10.1093/bioinformatics/btx411
Alexa A, Rahnenfuhrer J. (2020) topGO: Enrichment Analysis for Gene Ontology. R package version 2.46.0. https://bioconductor.org/packages/release/bioc/html/topGO.html
Walter W, Sanchez-Cabo F, Ricote M (2015) GOplot: an R package for visually combining expression data with functional analysis. Bioinformatics 31(17):2912–2914
doi: 10.1093/bioinformatics/btv300
Wickham H et al (2019) Welcome to the tidyverse. J Open Source Soft 4(43):1686. https://doi.org/10.21105/joss.01686
doi: 10.21105/joss.01686
Gehlenborg N (2019). UpSetR: a more scalable alternative to Venn and Euler diagrams for visualizing intersecting sets. R package version 1.4.0. https://CRAN.R-project.org/package=UpSetR
Brunson JC and Read QD (2020). ggalluvial: Alluvial Plots in “ggplot2”. R package version 0.12.3. http://corybrunson.github.io/ggalluvial/
Chen H (2018). VennDiagram: generate high-resolution Venn and Euler plots. R package version 1.6.20. https://CRAN.R-project.org/package=VennDiagram
Yan L (2021). ggvenn: Draw Venn Diagram by 'ggplot2'. R package version 0.1.8. https://CRAN.R-project.org/package=ggvenn
Gao C (2019). ggVennDiagram: A “ggplot2” implement of Venn diagram. R package version 0.3. https://CRAN.R-project.org/package=ggVennDiagram
Wilkinson L (2011). venneuler: Venn and Euler Diagrams. R package version 1.1-0. https://CRAN.R-project.org/package=venneuler
Larsson J (2020). _eulerr: area-proportional Euler and Venn diagrams with ellipses. R package version 6.1.0. https://cran.r-project.org/package=eulerr
Chaudhari AK, Chaudhary BR (2012) Meiotic chromosome behaviour and karyomorphology of Aloe vera (L.) Burm. f. Chromosom Bot 7(1):23–29
doi: 10.3199/iscb.7.23
Colas I, Darrier B, Arrieta M et al (2017) Observation of extensive chromosome Axis remodeling during the “diffuse-phase” of meiosis in large genome cereals. Front Plant Sci 8:1235
doi: 10.3389/fpls.2017.01235
Gómez JF, Wilson ZA (2012) Non-destructive staging of barley reproductive development for molecular analysis based upon external morphology. J Exp Bot 63(11):4085–4094
doi: 10.1093/jxb/ers092
Huerta-Cepas J, Szklarczyk D, Heller D et al (2019) eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses. Nucleic Acids Res 47(D1):D309–D314
doi: 10.1093/nar/gky1085
Törönen P, Medlar A, Holm L (2018) PANNZER2: a rapid functional annotation web server. Nucleic Acids Res 46(W1):W84–W88
doi: 10.1093/nar/gky350