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Spacer-Based Macroarrays for CRISPR Genotyping

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CRISPR

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1311))

Abstract

Macroarray-based analysis is a powerful and economic format to study variations in “clustered regularly interspaced short palindromic repeat (CRISPR)” loci in bacteria. To date, it was used almost exclusively for Mycobacterium tuberculosis and was named spoligotyping (spacer oligonucleotides typing). Here, we describe the pipeline of this approach that includes search of loci and selection of spacers, preparation of the membrane with immobilized probes and spoligotyping itself (PCR and reverse hybridization).

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Acknowledgements

We are grateful to Thierry Zozio, Elisabeth Streit and Julie Millet (Institut Pasteur de la Guadeloupe), Anna Vyazovaya and Olga Narvskaya (St. Petersburg Pasteur Institute) for helpful discussions. Igor Mokrousov gratefully acknowledges support from Russian Science Foundation (project 14-14-00292).

Author information

Authors and Affiliations

  1. Laboratory of Molecular Microbiology, St. Petersburg Pasteur Institute, 14 Mira Street, St. Petersburg, 197101, Russia

    Igor Mokrousov

  2. WHO Supranational TB Reference Laboratory, Tuberculosis & Mycobacteria Unit, Institut Pasteur de la Guadeloupe, Abymes, Guadeloupe, France

    Nalin Rastogi

Authors
  1. Igor Mokrousov
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  2. Nalin Rastogi
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Corresponding author

Correspondence to Igor Mokrousov .

Editor information

Editors and Affiliations

  1. Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden

    Magnus Lundgren

  2. Department of Molecular Biology MIMS, Umeå University, Umeå, Sweden

    Emmanuelle Charpentier

  3. Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand

    Peter C. Fineran

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Mokrousov, I., Rastogi, N. (2015). Spacer-Based Macroarrays for CRISPR Genotyping. In: Lundgren, M., Charpentier, E., Fineran, P. (eds) CRISPR. Methods in Molecular Biology, vol 1311. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-2687-9_7

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  • DOI: https://doi.org/10.1007/978-1-4939-2687-9_7

  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-2686-2

  • Online ISBN: 978-1-4939-2687-9

  • eBook Packages: Springer Protocols

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