  In recent years the publication of genome sequences for the Chinese hamster
and Chinese hamster ovary (CHO) cell lines have 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 characterise RNA expression (RNA-Seq). In this chapter we present a
computational pipeline for the analysis of CHO cell RNA-Seq data from the
Illumina platform to identify differentially expressed genes. The example data
and bioinformatics workflow required to run this analysis are freely available
at www.cgcdb.org/rnaseq_analysis_protocol.html.
