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Probe Design Strategies for Oligonucleotide Microarrays

  • Protocol
Book cover Microarray Technology

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1368))

Abstract

Oligonucleotide microarrays have been widely used for gene detection and/or quantification of gene expression in various samples ranging from a single organism to a complex microbial assemblage. The success of a microarray experiment, however, strongly relies on the quality of designed probes. Consequently, probe design is of critical importance and therefore multiple parameters should be considered for each probe in order to ensure high specificity, sensitivity, and uniformity as well as potentially quantitative power. Moreover, to assess the complete gene repertoire of complex biological samples such as those studied in the field of microbial ecology, exploratory probe design strategies must be also implemented to target not-yet-described sequences. To design such probes, two algorithms, KASpOD and HiSpOD, have been developed and they are available via two user-friendly web services. Here, we describe the use of this software necessary for the design of highly effective probes especially in the context of microbial oligonucleotide microarrays by taking into account all the crucial parameters.

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Acknowledgements

This work was supported by the French “Direction Générale de l’Armement” (DGA) and the programme Investissements d’avenir AMI 2011 VALTEX.

Author information

Authors and Affiliations

  1. Université d’Auvergne, EA 4678, CIDAM, Clermont Université, BP 10448, F-63000, Clermont-Ferrand, France

    Nicolas Parisot, Eric Peyretaillade & Pierre Peyret

  2. Génie et Microbiologie des Procédés Alimentaires, Centre de Biotechnologies Agro-Industrielles, INRA, AgroParisTech, UMR 782, Thiverval-Grignon, France

    Eric Dugat-Bony

  3. Genomic Platform and R&D, Genoscreen, Campus de l’Institut Pasteur, Lille, France

    Jérémie Denonfoux

  4. CRRI, Clermont Université, F-63177, Aubière, France

    Antoine Mahul

Authors
  1. Nicolas Parisot
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  2. Eric Peyretaillade
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  3. Eric Dugat-Bony
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  4. Jérémie Denonfoux
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  5. Antoine Mahul
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  6. Pierre Peyret
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Corresponding author

Correspondence to Pierre Peyret .

Editor information

Editors and Affiliations

  1. Department of Chemistry, Simon Fraser University, Burnaby, British Columbia, Canada

    Paul C.H. Li

  2. Dept. of Chemistry, Simon Fraser University, Burnaby, British Columbia, Canada

    Abootaleb Sedighi

  3. Department of Biomedical Engineering, University of British Columbia, Vancouver, British Columbia, Canada

    Lin Wang

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Parisot, N., Peyretaillade, E., Dugat-Bony, E., Denonfoux, J., Mahul, A., Peyret, P. (2016). Probe Design Strategies for Oligonucleotide Microarrays. In: Li, P., Sedighi, A., Wang, L. (eds) Microarray Technology. Methods in Molecular Biology, vol 1368. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-3136-1_6

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  • DOI: https://doi.org/10.1007/978-1-4939-3136-1_6

  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-3135-4

  • Online ISBN: 978-1-4939-3136-1

  • eBook Packages: Springer Protocols

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