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

  • Samuel E. Barnett
  • Nicholas D. Youngblut
  • Daniel H. BuckleyEmail author
Protocol
Part of the Methods in Molecular Biology book series (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.

Key words

DNA-SIP Stable isotope probing High throughput sequencing 

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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  • Samuel E. Barnett
    • 1
  • Nicholas D. Youngblut
    • 2
  • Daniel H. Buckley
    • 1
    Email author
  1. 1.School of Integrative Plant ScienceCornell UniversityIthacaUSA
  2. 2.Department of Microbiome ScienceMax Planck Institute for Developmental BiologyTübingenGermany

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