Bulk and Single-Cell RNA-Seq Analyses for Studies of Spermatogonia

Methods Mol Biol. 2023:2656:37-70. doi: 10.1007/978-1-0716-3139-3_4.

Abstract

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.

Keywords: Bioinformatics; Bulk RNA-seq; Single-cell RNA-seq; Spermatogenesis.

Publication types

  • Research Support, U.S. Gov't, Non-P.H.S.
  • Research Support, N.I.H., Extramural

MeSH terms

  • Animals
  • Gene Expression Profiling / methods
  • Male
  • Mammals
  • RNA-Seq
  • Sequence Analysis, RNA / methods
  • Single-Cell Analysis / methods
  • Single-Cell Gene Expression Analysis*
  • Spermatogonia*
  • Testis
  • Transcriptome