Bulk and Single-Cell RNA-Seq Analyses for Studies of Spermatogonia.
Bioinformatics
Bulk RNA-seq
Single-cell RNA-seq
Spermatogenesis
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:
2023
2023
Historique:
medline:
1
6
2023
pubmed:
30
5
2023
entrez:
30
5
2023
Statut:
ppublish
Résumé
Robust methods have been developed that leverage next-generation sequencing (NGS) to measure abundance of all mRNAs (RNA-seq) in samples as small as individual cells in order to study the testicular transcriptome in mammals. In this chapter, we present robust options for implementing bioinformatics workflows for the analysis of bulk RNA-seq from aggregate samples of hundreds to millions of cells and single-cell RNA-seq from individual cells. We also provide detailed protocols for using the R packages DESeq2 and Seurat, important parameters for successful implementation, and considerations for drawing conclusions from the results.
Identifiants
pubmed: 37249866
doi: 10.1007/978-1-0716-3139-3_4
pmc: PMC10353477
mid: NIHMS1912190
doi:
Types de publication
Journal Article
Research Support, U.S. Gov't, Non-P.H.S.
Research Support, N.I.H., Extramural
Langues
eng
Sous-ensembles de citation
IM
Pagination
37-70Subventions
Organisme : NIMHD NIH HHS
ID : G12 MD007591
Pays : United States
Organisme : NICHD NIH HHS
ID : R01 HD090007
Pays : United States
Organisme : NIDA NIH HHS
ID : U01 DA054170
Pays : United States
Informations de copyright
© 2023. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.
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