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Application of a CAGE Method to an Avian Development Study

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Avian and Reptilian Developmental Biology

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1650))

Abstract

Cap analysis of gene expression (CAGE) is a convenient approach for genome-wide identification of promoter regions at single base-pair resolution level and accurate expression estimation of the corresponding transcripts. Depending on the initial biomaterial amount and sequencing technology, different computational pipelines for data processing are available, as well as variations of the CAGE protocol that improve sensitivity and accuracy. Therefore, this chapter elucidates the key steps of sample preparation, sequencing, and data analysis via an example of a promoter expression estimation study in chicken development. We also describe the applicability of this approach for studying other avian and reptilian species.

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Acknowledgments

This work was supported by the Russian Science Foundation, grant â„–14-44-00022.

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Authors and Affiliations

  1. Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russia

    Ruslan Deviatiiarov & Oleg Gusev

  2. Division of Genomic Technologies, Center for Life Science Technologies (CLST), RIKEN, Yokohama, Japan

    Marina Lizio & Oleg Gusev

  3. Omics Science Center (OSC), RIKEN, Yokohama, Japan

    Marina Lizio

  4. Preventive Medicine and Diagnosis Innovation Program, RIKEN, Yokohama, Japan

    Oleg Gusev

  5. RIKEN Innovation Center, Wako, Japan

    Oleg Gusev

Authors
  1. Ruslan Deviatiiarov
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  2. Marina Lizio
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  3. Oleg Gusev
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Corresponding author

Correspondence to Oleg Gusev .

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Editors and Affiliations

  1. IRCMS, Kumamoto University, Kumamoto, Kumamoto, Japan

    Guojun Sheng

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Deviatiiarov, R., Lizio, M., Gusev, O. (2017). Application of a CAGE Method to an Avian Development Study. In: Sheng, G. (eds) Avian and Reptilian Developmental Biology. Methods in Molecular Biology, vol 1650. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7216-6_6

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  • DOI: https://doi.org/10.1007/978-1-4939-7216-6_6

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-7215-9

  • Online ISBN: 978-1-4939-7216-6

  • eBook Packages: Springer Protocols

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