RNA extraction protocol from low-biomass bacterial Nitrosomonas europaea and Nitrobacter winogradskyi cultures for whole transcriptome studies

Tom Verbeelen, Rob Van Houdt, Natalie Leys, Ramon Ganigué, Felice Mastroleo

    Research outputpeer-review

    Abstract

    RNA-sequencing for whole transcriptome analysis requires high-quality RNA in adequate amounts, which can be difficult to generate with low-biomass-producing bacteria where sample volume is limited. We present an RNA extraction protocol for low-biomass-producing autotrophic bacteria Nitrosomonas europaea and Nitrobacter winogradskyi cultures. We describe steps for sample collection, lysozyme-based enzymatic lysis, and a commercial silica-column-based RNA extraction. We then detail evaluation of RNA yield and quality for downstream applications such as RNA-Seq. For complete details on the use and execution of this protocol, please refer to Verbeelen et al.

    Original languageEnglish
    Article number102358
    Number of pages9
    JournalSTAR Protocols
    Volume4
    Issue number3
    DOIs
    StatePublished - 15 Sep 2023

    ASJC Scopus subject areas

    • Biochemistry, Genetics and Molecular Biology(all)
    • Immunology and Microbiology(all)
    • Neuroscience(all)

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