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Sequencing of Genomes from Environmental Single Cells

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Next Generation Sequencing

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

Abstract

Sequencing of single bacterial and archaeal cells is an important methodology that provides access to the genetic makeup of uncultivated microorganisms. We here describe the high-throughput fluorescence-activated cell sorting-based isolation of single cells from the environment, their lysis and strand displacement-mediated whole genome amplification. We further outline 16S rRNA gene sequence-based screening of single-cell amplification products, their preparation for Illumina sequencing libraries, and finally propose computational methods for read and contig level quality control of the resulting sequence data.

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Acknowledgment

The work conducted by the U.S. Department of Energy Joint Genome Institute, a DOE Office of Science User Facility, is supported under Contract No. DE-AC02-05CH11231. We would like to thank Bill Andreopoulos for his assistance in preparing Fig. 2.

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Authors and Affiliations

  1. Department of Energy, Joint Genome Institute, Walnut Creek, CA, USA

    Robert M. Bowers, Janey Lee & Tanja Woyke

Authors
  1. Robert M. Bowers
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  2. Janey Lee
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  3. Tanja Woyke
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Corresponding author

Correspondence to Tanja Woyke .

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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Bowers, R.M., Lee, J., Woyke, T. (2018). Sequencing of Genomes from Environmental Single Cells. 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_8

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  • DOI: https://doi.org/10.1007/978-1-4939-7514-3_8

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-7512-9

  • Online ISBN: 978-1-4939-7514-3

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