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Data Analysis for DNA Stable Isotope Probing Experiments Using Multiple Window High-Resolution SIP

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Stable Isotope Probing

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2046))

Abstract

DNA stable isotope probing (DNA-SIP) allows for the identification of microbes that assimilate isotopically labeled substrates into DNA. Here we describe the analysis of sequencing data using the multiple window high-resolution DNA-SIP method (MW-HR-SIP). MW-HR-SIP has improved accuracy over other methods and is easily implemented on the statistical platform R. We also discuss key experimental parameters to consider when designing DNA-SIP experiments and how these parameters affect accuracy of analysis.

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Author information

Authors and Affiliations

  1. School of Integrative Plant Science, Cornell University, Ithaca, NY, USA

    Samuel E. Barnett & Daniel H. Buckley

  2. Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen, Germany

    Nicholas D. Youngblut

Authors
  1. Samuel E. Barnett
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  2. Nicholas D. Youngblut
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  3. Daniel H. Buckley
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Corresponding author

Correspondence to Daniel H. Buckley .

Editor information

Editors and Affiliations

  1. School of Biological Sciences, University of Southampton, Southampton, UK

    Marc G. Dumont

  2. School of Biological Sciences, University of Southampton, Southampton, UK

    Marcela Hernández García

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Barnett, S.E., Youngblut, N.D., Buckley, D.H. (2019). Data Analysis for DNA Stable Isotope Probing Experiments Using Multiple Window High-Resolution SIP. In: Dumont, M., Hernández García, M. (eds) Stable Isotope Probing. Methods in Molecular Biology, vol 2046. Humana, New York, NY. https://doi.org/10.1007/978-1-4939-9721-3_9

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  • DOI: https://doi.org/10.1007/978-1-4939-9721-3_9

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-4939-9720-6

  • Online ISBN: 978-1-4939-9721-3

  • eBook Packages: Springer Protocols

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