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Oral Biology pp 249–278Cite as

Strategy for RNA-Seq Experimental Design and Data Analysis

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

Abstract

Ribonucleic acids (RNAs) are fundamental molecules that control regulation and expression of the genome and therefore the function of a cell. Robust analysis and quantification of RNA transcripts hold critical importance in understanding cell function, altered phenotypes in different biological context, for understanding and targeting diseases. The development of RNA-sequencing (RNA-Seq) now provides opportunities to analyze the expression and function of RNA molecules at an unprecedented scale. However, the strategy for RNA-Seq experimental design and data analysis can substantially differ depending on the biological application. The design choice could also have significant impact for downstream results and interpretation of data. Here we describe key critical considerations required for RNA-Seq experimental design and also describe a step-by-step bioinformatics workflow detailing the different steps required for RNA-Seq data analysis. We believe this article will be a valuable guide for designing and analyzing RNA-Seq data to address a wide range of different biological questions.

Key words

  • RNA-Seq
  • Gene expression
  • Transcript
  • Sequencing
  • Alignment
  • Sequence reads

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Acknowledgments

We would like to thank the Rutherford Discovery Fellowship Program (Royal Society of New Zealand) for supporting AC’s current position and the Dunedin School of Medicine for supporting our work.

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Authors and Affiliations

  1. Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand

    Gregory Gimenez, Peter A. Stockwell, Euan J. Rodger & Aniruddha Chatterjee

  2. UPES University, School of Health Sciences, Dehradun, India

    Aniruddha Chatterjee

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  1. Gregory Gimenez
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  2. Peter A. Stockwell
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  3. Euan J. Rodger
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  4. Aniruddha Chatterjee
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Corresponding authors

Correspondence to Gregory Gimenez or Aniruddha Chatterjee .

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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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Gimenez, G., Stockwell, P.A., Rodger, E.J., Chatterjee, A. (2023). Strategy for RNA-Seq Experimental Design and Data Analysis. 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_16

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