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The Tumor Microenvironment pp 311–337Cite as

RNA-Seq as a Tool to Study the Tumor Microenvironment

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Part of the book series: Methods in Molecular Biology ((MIMB,volume 1458))

Abstract

The transcriptome is composed of different types of RNA molecules including mRNAs, tRNAs, rRNAs, and other noncoding RNAs that are found inside a cell at a given time. Analyzing transcriptome patterns can shed light on the functional state of the cell as well as on the dynamics of cellular behavior associated with genomic and environmental changes. Likewise, transcriptome analysis has been a major help in solving biological issues and understanding the molecular basis of many diseases including human cancers. Specifically, since targeted and whole genome sequencing studies are becoming more common in identifying the driving factors of cancer, a comprehensive and high-resolution analysis of the transcriptome, as provided by RNA-Sequencing (RNA-Seq), plays a key role in investigating the functional relevance of the identified genomic aberrations. Here, we describe experimental procedures of RNA-Seq and downstream data processing and analysis, with a focus on the identification of abnormally expressed transcripts and genes.

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Author information

Authors and Affiliations

  1. Department of Human Genetics, McGill University, Montreal, QC, Canada

    Pudchalaluck Panichnantakul, Guillaume Bourque & Yasser Riazalhosseini

  2. McGill University and Genome Quebec Innovation Centre, Montreal, QC, Canada

    Pudchalaluck Panichnantakul, Mathieu Bourgey, Alexandre Montpetit, Guillaume Bourque & Yasser Riazalhosseini

Authors
  1. Pudchalaluck Panichnantakul
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  2. Mathieu Bourgey
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  3. Alexandre Montpetit
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  4. Guillaume Bourque
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  5. Yasser Riazalhosseini
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Corresponding author

Correspondence to Yasser Riazalhosseini .

Editor information

Editors and Affiliations

  1. Lady Davis Institute for Medical Research, Montreal, Québec, Canada

    Josie Ursini-Siegel

  2. Goodman Cancer Research Centre, McGill University, Montreal, Québec, Canada

    Nicole Beauchemin

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Panichnantakul, P., Bourgey, M., Montpetit, A., Bourque, G., Riazalhosseini, Y. (2016). RNA-Seq as a Tool to Study the Tumor Microenvironment. In: Ursini-Siegel, J., Beauchemin, N. (eds) The Tumor Microenvironment. Methods in Molecular Biology, vol 1458. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-3801-8_22

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  • DOI: https://doi.org/10.1007/978-1-4939-3801-8_22

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-3799-8

  • Online ISBN: 978-1-4939-3801-8

  • eBook Packages: Springer Protocols

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