Transcriptomic Analysis of Human Naïve and Primed Pluripotent Stem Cells

Methods Mol Biol. 2022;2416:213-237. doi: 10.1007/978-1-0716-1908-7_14.


Over the last decade, RNA-Sequencing (RNA-Seq) has revolutionized the field of transcriptomics due to its sheer advantage over previous technologies for studying gene expression. Even the domain of stem cell bioinformatics has benefited from these advancements. It has helped look deeper into how the process of pluripotency is maintained by stem cells and how it may be exploited for application in regenerative medicine. However, as it is still an evolving technology, there is no single accepted protocol for RNA-Seq data analysis. From a wide array of tools and/or algorithms available for the purpose, researchers tend to develop a pipeline that is best suited for their sample, experimental design, and computational power. In this tutorial, we describe a pipeline based on open-source tools to analyze RNA-Seq data from naïve and primed state human pluripotent stem cell samples. Precisely, we show how RNA-Seq data can be downloaded from databases, processed, and used to identify differentially expressed genes and construct a co-expression network. Further, we also show how the list of interesting genes obtained from differential expression testing or co-expression network be analyzed to gain biological insights.

Keywords: Bioinformatics analysis; Co-expression network; Differential gene expression; Human pluripotency; RNA-Seq; Read alignment; Read quantification; Sample clustering.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Computational Biology
  • Gene Expression Profiling
  • Humans
  • Pluripotent Stem Cells*
  • Sequence Analysis, RNA
  • Transcriptome*