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Extending and Running the Mosquito Small RNA Genomics Resource Pipeline

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piRNA

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2509))

Abstract

The Mosquito Small RNA Genomics (MSRG) resource is a repository of analyses on the small RNA transcriptomes of mosquito cell cultures and somatic and gonadal tissues. This resource allows for comparing the regulation dynamics of small RNAs generated from transposons and viruses across mosquito species. This chapter covers the procedures to set up the MSRG resource pipeline as a new installation by detailing the necessary collection of genome reference and annotation files and lists of microRNAs (miRNAs) hairpin sequences, transposon repeats consensus sequences, and virus genome sequences. Proper execution of the MSRG resource pipeline yields outputs amenable to biologists to further analyze with desktop and spreadsheet software to gain insights into the balance between arthropod endogenous small RNA populations and the proportions of virus-derived small RNAs that include Piwi-interacting RNAs (piRNAs) and endogenous small interfering RNAs (siRNAs).

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Acknowledgements

We thank the patience of the editors for pandemic-related extensions and Augustine Abaris from Boston University Research Computing Services for assistance with the setup of the singularity image. This study was also supported by Boston University School of Medicine Startup funds, the BU Genome Science Institute, the Wing-Tat Lee foundation, and the NIH grant fund R01-GM135215 to N.C.L.

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Authors and Affiliations

  1. Boston University School of Medicine, Department of Biochemistry, Boston University Bioinformatics Program, Boston, MA, USA

    Gargi Dayama & Nelson C. Lau

  2. Boston University Research Computing Services, Information Services and Technology, Boston, MA, USA

    Katia Bulekova

Authors
  1. Gargi Dayama
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  2. Katia Bulekova
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  3. Nelson C. Lau
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Corresponding author

Correspondence to Nelson C. Lau .

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Editors and Affiliations

  1. Center for Integrative Medical Sciences, RIKEN, Yokohama, Kanagawa, Japan

    Nicholas F. Parrish

  2. Department of Molecular Biology, Keio University School of Medicine, Tokyo, Japan

    Yuka W. Iwasaki

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© 2022 The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature

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Dayama, G., Bulekova, K., Lau, N.C. (2022). Extending and Running the Mosquito Small RNA Genomics Resource Pipeline. In: Parrish, N.F., Iwasaki, Y.W. (eds) piRNA. Methods in Molecular Biology, vol 2509. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-2380-0_20

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  • DOI: https://doi.org/10.1007/978-1-0716-2380-0_20

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-2379-4

  • Online ISBN: 978-1-0716-2380-0

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