A Bioinformatics Pipeline for the Identification of CHO Cell Differential Gene Expression from RNA-Seq Data

In recent years, the publication of genome sequences for the Chinese hamster and Chinese hamster ovary (CHO) cell lines has facilitated study of these biopharmaceutical cell factories with unprecedented resolution. Our understanding of the CHO cell transcriptome, in particular, has rapidly advanced through the application of next-generation sequencing (NGS) technology to characterize RNA expression (RNA-Seq). In this chapter, researchers from the National Institute for Bioprocessing Research and Training, Ireland present a computational pipeline for the analysis of CHO cell RNA-Seq data from the Illumina platform to identify differentially expressed genes.

RNA-Seq bioinformatics protocol overview

(a) Quality assessment of raw sequencing data and preprocessing of reads to correct potential issues including low base quality. (b) Alignment of reads to the Chinese hamster reference sequence and calculation of global mapping quality. (c) Counting reads aligned to each protein-coding gene. (d) Differential expression analysis

Availability – The example data and bioinformatics workflow required to run this analysis are freely available at www.cgcdb.org/rnaseq_analysis_protocol.html