Sample Preparation and Differential Gene Expression Analysis of Human Cancer Cell Lines by RNA Sequencing

Dmitry Leshchiner; Tommy V Vo; Sachi Horibata

doi:10.1007/978-1-0716-3163-8_3

Sample Preparation and Differential Gene Expression Analysis of Human Cancer Cell Lines by RNA Sequencing

Methods Mol Biol. 2023:2660:23-41. doi: 10.1007/978-1-0716-3163-8_3.

Authors

Dmitry Leshchiner^{1

2}, Tommy V Vo³, Sachi Horibata^{4

5}

Affiliations

¹ Precision Health Program, Michigan State University, East Lansing, MI, USA.
² Department of Pharmacology and Toxicology, College of Human Medicine, Michigan State University, East Lansing, MI, USA.
³ Department of Biochemistry and Molecular Biology, College of Human Medicine, Michigan State University, East Lansing, MI, USA. votommyv@msu.edu.
⁴ Precision Health Program, Michigan State University, East Lansing, MI, USA. horibat2@msu.edu.
⁵ Department of Pharmacology and Toxicology, College of Human Medicine, Michigan State University, East Lansing, MI, USA. horibat2@msu.edu.

PMID: 37191788
DOI: 10.1007/978-1-0716-3163-8_3

Abstract

RNA sequencing (RNA-seq) is a method used for the high-throughput quantification of mRNA in a biological sample. It is widely used to investigate differential gene expression between drug-resistant and sensitive cancers to identify genetic mediators of drug resistance. Here, we describe a comprehensive experimental and bioinformatic pipeline to isolate mRNA from human cell lines, prepare mRNA libraries for next-generation sequencing, and perform post-sequencing bioinformatics analyses.

Keywords: Gene expression; RNA-sequencing; Transcriptomics; mRNA.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Cell Line
Computational Biology* / methods
Gene Expression Profiling / methods
High-Throughput Nucleotide Sequencing / methods
Humans
Neoplasms* / genetics
RNA / genetics
RNA, Messenger / genetics
Sequence Analysis, RNA / methods
Transcriptome

Substances

RNA, Messenger
RNA