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, 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.
Transcriptomics RNA-Seq Differential gene expression Chinese hamster ovary cells Biopharmaceutical manufacture Systems biotechnology
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The authors gratefully acknowledge funding from Science Foundation Ireland (grant refs: 13/SIRG/2084 and 13/IA/1963) and the eCHO systems Marie Curie ITN programme (grant ref.: 642663).
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