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


    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
    Issue number3
    StatePublished - 15 Sep 2023

    ASJC Scopus subject areas

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

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