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A Workflow Guide to RNA-seq Analysis of Chaperone Function and Beyond

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Book cover Chaperones

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1709))

Abstract

RNA sequencing (RNA-seq) is a powerful method of transcript analysis that allows for the sequence identification and quantification of cellular transcripts. RNA-seq has many applications including differential gene expression (DE) analysis, gene fusion detection, allele-specific expression, isoform and splice variant quantification, and identification of novel genes. These applications can be used for downstream systems biology analyses such as gene ontology analysis to provide insights into cellular processes altered between biological conditions. Given the wide range of signaling pathways subject to chaperone activity as well as numerous chaperone functions in RNA metabolism, RNA-seq may provide a valuable tool for the study of chaperone proteins in biology and disease. This chapter outlines an example RNA-seq workflow to determine differentially expressed (DE) genes between two or more sample conditions and provides some considerations for RNA-seq experimental design.

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Acknowledgments

We thank Thiago De Borges (BIDMC, Harvard Medical School) for critical reading of this chapter.

Declaration of Interest: Kristina M Holton is currently a Campus Champion for the XSEDE project.

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Author notes

  1. Benjamin J. Lang and Kristina M. Holton contributed equally to this work.

Authors and Affiliations

  1. Department of Radiation Oncology, Beth Israel Deaconess Medical Center, Harvard Medical School, 330 Brookline Avenue, Boston, MA, 02215, USA

    Benjamin J. Lang & Stuart K. Calderwood

  2. Research Computing, Harvard Medical School, Boston, MA, USA

    Kristina M. Holton

  3. Department of Medicine, Boston University School of Medicine, Boston, MA, USA

    Jianlin Gong

Authors
  1. Benjamin J. Lang
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  2. Kristina M. Holton
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  3. Jianlin Gong
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  4. Stuart K. Calderwood
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Corresponding author

Correspondence to Benjamin J. Lang .

Editor information

Editors and Affiliations

  1. Department of Radiation, Oncology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA

    Stuart K. Calderwood

  2. Department of Urology, Weis Center for Research, Geisinger Clinic, Danville, Pennsylvania, USA

    Thomas L. Prince

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Lang, B.J., Holton, K.M., Gong, J., Calderwood, S.K. (2018). A Workflow Guide to RNA-seq Analysis of Chaperone Function and Beyond. In: Calderwood, S., Prince, T. (eds) Chaperones. Methods in Molecular Biology, vol 1709. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7477-1_18

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  • DOI: https://doi.org/10.1007/978-1-4939-7477-1_18

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-7476-4

  • Online ISBN: 978-1-4939-7477-1

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