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

Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1603)

Abstract

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.

Key words

Transcriptomics RNA-Seq Differential gene expression Chinese hamster ovary cells Biopharmaceutical manufacture Systems biotechnology 

Notes

Acknowledgments

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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Copyright information

© Springer Science+Business Media LLC 2017

Authors and Affiliations

  1. 1.National Institute for Bioprocessing Research and TrainingCo. DublinIreland
  2. 2.National Institute for Cellular BiotechnologyDublin City UniversityDublin 9Ireland

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