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RNA Sequencing Analysis of Saliva exRNA

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Oral Biology

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2588))

Abstract

Next-generation sequencing (NGS) methodologies are rapidly developing. However, RNA Sequencing of saliva is challenging due to low abundance and integrity of extracellular RNA, as well as large amounts of bacterial RNAs that may be encountered in saliva. In addition, the literature about human salivary extracellular RNA is very scarce. Therefore, in our chapter, we present the most appropriate protocols for saliva collection, pre- and post-processing, including bioinformatic analysis of salivary RNA Sequencing data. However, the choice of the proper method for RNA extraction, cDNA library preparation, and computational pipeline can make a significant impact on the final quality of data and their interpretation.

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Acknowledgments

This work was supported by the Public Health Service (PHS) grant from the National Institutes of Health (NIH): UH3 TR000923, UG3/UH3 TR002978, 5 R25 DE030117, SEED grant from the UCLA Jonsson Comprehensive Cancer Center / Ali Jassim Family Cancer Research Fund (Y.K.), the QCBio Collaboratory Fellowship 2019-2022 from the Institute for Quantitative & Computational Biosciences at the University of California, Los Angeles (K.E.K-U), and UCLA Jonsson Comprehensive Cancer Center’s (JCCC) Postdoctoral Fellowship Award (K.E.K-U).

Conflicts of Interest

David Wong is consultant to GlaxoSmithKlein, PeriRx, Wrigley, and Colgate-Palmolive. David Wong holds equity in RNAmeTRIX Inc. and Liquid Diagnostics LLC. The University of California also holds equity in RNAmeTRIX. None of the other authors have a conflict of interest in relation to this study.

Author information

Authors and Affiliations

  1. Center for Oral and Head/Neck Oncology Research, UCLA School of Dentistry, University of California at Los Angeles, Los Angeles, CA, USA

    Karolina Elżbieta Kaczor-Urbanowicz & David T. W. Wong

  2. UCLA Institute for Quantitative and Computational Biosciences, University of California at Los Angeles, Los Angeles, CA, USA

    Karolina Elżbieta Kaczor-Urbanowicz

  3. UCLA Section of Orthodontics, University of California at Los Angeles, Los Angeles, CA, USA

    Karolina Elżbieta Kaczor-Urbanowicz

  4. Section of Biosystems and Function, UCLA School of Dentistry, University of California at Los Angeles, Los Angeles, CA, USA

    Karolina Elżbieta Kaczor-Urbanowicz & David T. W. Wong

  5. UCLA’s Jonsson Comprehensive Cancer Center, Los Angeles, CA, USA

    David T. W. Wong

Authors
  1. Karolina Elżbieta Kaczor-Urbanowicz
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  2. David T. W. Wong
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Corresponding author

Correspondence to David T. W. Wong .

Editor information

Editors and Affiliations

  1. School of Dentistry, The University of Queensland, Herston, QLD, Australia

    Gregory J. Seymour

  2. School of Dentistry, The University of Queensland, Herston, QLD, Australia

    Mary P. Cullinan

  3. Faculty of Dentistry, University of Otago, Dunedin, New Zealand

    Nicholas C.K. Heng

  4. Faculty of Dentistry, University of Otago, Dunedin, New Zealand

    Paul R. Cooper

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© 2023 The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature

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Kaczor-Urbanowicz, K.E., Wong, D.T.W. (2023). RNA Sequencing Analysis of Saliva exRNA. In: Seymour, G.J., Cullinan, M.P., Heng, N.C., Cooper, P.R. (eds) Oral Biology. Methods in Molecular Biology, vol 2588. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-2780-8_1

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  • DOI: https://doi.org/10.1007/978-1-0716-2780-8_1

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-2779-2

  • Online ISBN: 978-1-0716-2780-8

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