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

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Heterologous Protein Production in CHO Cells

Part of the book series: Methods in Molecular Biology ((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.

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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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Authors and Affiliations

  1. National Institute for Bioprocessing Research and Training, Fosters Avenue, Blackrock, Co. Dublin, Ireland

    Craig Monger, Krishna Motheramgari, John McSharry & Colin Clarke

  2. National Institute for Cellular Biotechnology, Dublin City University, Dublin 9, Ireland

    Craig Monger, Krishna Motheramgari & Niall Barron

Authors
  1. Craig Monger
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  2. Krishna Motheramgari
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  3. John McSharry
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  4. Niall Barron
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  5. Colin Clarke
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Corresponding author

Correspondence to Colin Clarke .

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Editors and Affiliations

  1. National Institute for Cellular Biotechnology, Dublin City University, Dublin, Ireland

    Paula Meleady

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Monger, C., Motheramgari, K., McSharry, J., Barron, N., Clarke, C. (2017). A Bioinformatics Pipeline for the Identification of CHO Cell Differential Gene Expression from RNA-Seq Data. In: Meleady, P. (eds) Heterologous Protein Production in CHO Cells. Methods in Molecular Biology, vol 1603. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-6972-2_11

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  • DOI: https://doi.org/10.1007/978-1-4939-6972-2_11

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-6971-5

  • Online ISBN: 978-1-4939-6972-2

  • eBook Packages: Springer Protocols

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