Protocol for identifying differentially expressed genes using the RumBall RNA-seq analysis platform

Luis Augusto Eijy Nagai; Seohyun Lee; Ryuichiro Nakato

doi:10.1016/j.xpro.2024.102926

Protocol for identifying differentially expressed genes using the RumBall RNA-seq analysis platform

STAR Protoc. 2024 Mar 15;5(1):102926. doi: 10.1016/j.xpro.2024.102926. Epub 2024 Mar 10.

Authors

Luis Augusto Eijy Nagai¹, Seohyun Lee², Ryuichiro Nakato³

Affiliations

¹ Laboratory of Computational Genomics, Institute for Quantitative Biosciences, The University of Tokyo, Bunkyo, Tokyo 113-0032, Japan. Electronic address: nagai@iqb.u-tokyo.ac.jp.
² Laboratory of Computational Genomics, Institute for Quantitative Biosciences, The University of Tokyo, Bunkyo, Tokyo 113-0032, Japan.
³ Laboratory of Computational Genomics, Institute for Quantitative Biosciences, The University of Tokyo, Bunkyo, Tokyo 113-0032, Japan. Electronic address: rnakato@iqb.u-tokyo.ac.jp.

Abstract

Here, we present a protocol for the identification of differentially expressed genes through RNA sequencing analysis. Starting with FASTQ files from public datasets, this protocol leverages RumBall within a self-contained Docker system. We describe the steps for software setup, obtaining data, read mapping, sample normalization, statistical modeling, and gene ontology enrichment. We then detail procedures for interpreting results with plots and tables. RumBall internally utilizes popular tools, ensuring a comprehensive understanding of the analysis process.

Keywords: Bioinformatics; RNA-seq; Sequence analysis.

Publication types

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

MeSH terms

Gene Expression
Gene Expression Profiling* / methods
RNA-Seq
Sequence Analysis, RNA / methods
Software*