RNA Sequencing Analysis of Saliva exRNA

Karolina Elżbieta Kaczor-Urbanowicz; David T W Wong

doi:10.1007/978-1-0716-2780-8_1

RNA Sequencing Analysis of Saliva exRNA

Methods Mol Biol. 2023:2588:3-11. doi: 10.1007/978-1-0716-2780-8_1.

Authors

Karolina Elżbieta Kaczor-Urbanowicz^{1

2

3

4}, David T W Wong^{5

6

7}

Affiliations

¹ Center for Oral and Head/Neck Oncology Research, UCLA School of Dentistry, University of California at Los Angeles, Los Angeles, CA, USA.
² UCLA Institute for Quantitative and Computational Biosciences, University of California at Los Angeles, Los Angeles, CA, USA.
³ UCLA Section of Orthodontics, University of California at Los Angeles, Los Angeles, CA, USA.
⁴ Section of Biosystems and Function, UCLA School of Dentistry, University of California at Los Angeles, Los Angeles, CA, USA.
⁵ Center for Oral and Head/Neck Oncology Research, UCLA School of Dentistry, University of California at Los Angeles, Los Angeles, CA, USA. dtww@ucla.edu.
⁶ Section of Biosystems and Function, UCLA School of Dentistry, University of California at Los Angeles, Los Angeles, CA, USA. dtww@ucla.edu.
⁷ UCLA's Jonsson Comprehensive Cancer Center, Los Angeles, CA, USA. dtww@ucla.edu.

PMID: 36418678
DOI: 10.1007/978-1-0716-2780-8_1

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.

Keywords: Bioinformatic analysis; RNA Sequencing; Saliva; Salivary RNAs; Transcriptome.

Publication types

Research Support, Non-U.S. Gov't
Research Support, N.I.H., Extramural

MeSH terms

Gene Library
High-Throughput Nucleotide Sequencing*
Humans
RNA, Bacterial / genetics
Saliva*
Sequence Analysis, RNA

Substances

RNA, Bacterial

Abstract

Publication types

MeSH terms

Substances

Grants and funding