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Next Generation Sequencing pp 175–201Cite as

A Bloody Primer: Analysis of RNA-Seq from Tissue Admixtures

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Part of the book series: Methods in Molecular Biology ((MIMB,volume 1712))

Abstract

RNA sequencing is a powerful technology that allows for unbiased profiling of the entire transcriptome. The analysis of transcriptome profiles from heterogeneous tissues, cell admixtures with relative proportions that can vary several fold across samples, poses a significant challenge. Blood is perhaps the most egregious example. Here, we describe in detail a computational pipeline for RNA-Seq data preparation and statistical analysis, with development of a means of estimating the cell type composition of blood samples from their bulk RNA-Seq profiles. We also illustrate the importance of adjusting for the potential confounding effect of cellular heterogeneity in the context of statistical inference in a whole blood RNA-Seq dataset.

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Author information

Authors and Affiliations

  1. Prevention of Organ Failure (PROOF) Centre of Excellence, Centre for Heart Lung Innovation, University of British Columbia, St. Paul’s Hospital, Vancouver, BC, Canada

    Casey P. Shannon, Chen Xi Yang & Scott J. Tebbutt

  2. Division of Respiratory Medicine, Department of Medicine, University of British Columbia, St. Paul’s Hospital, Vancouver, BC, Canada

    Scott J. Tebbutt

Authors
  1. Casey P. Shannon
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  2. Chen Xi Yang
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  3. Scott J. Tebbutt
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Corresponding authors

Correspondence to Casey P. Shannon or Scott J. Tebbutt .

Editor information

Editors and Affiliations

  1. Next Generation Sequencing and Microarray Core Facility, The Scripps Research Institute, La Jolla, California, USA

    Steven R. Head

  2. Next Generation Sequencing and Microarray Core Facility, The Scripps Research Institute, La Jolla, California, USA

    Phillip Ordoukhanian

  3. Department of Molecular Medicine, The Scripps Research Institute Center for Organ and Cell Transplantation, La Jolla, California, USA

    Daniel R. Salomon

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Shannon, C.P., Yang, C.X., Tebbutt, S.J. (2018). A Bloody Primer: Analysis of RNA-Seq from Tissue Admixtures. In: Head, S., Ordoukhanian, P., Salomon, D. (eds) Next Generation Sequencing. Methods in Molecular Biology, vol 1712. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7514-3_12

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  • DOI: https://doi.org/10.1007/978-1-4939-7514-3_12

  • Published:

  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-7512-9

  • Online ISBN: 978-1-4939-7514-3

  • eBook Packages: Springer Protocols

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