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

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

  • STAR Protoc. 2023 Jun 21;4(3):102358. doi: 10.1016/j.xpro.2023.102358.
Tom Verbeelen 1,  Rob Van Houdt 2,  Natalie Leys 2,  Ramon Ganigué 3,  Felice Mastroleo 4
Affiliations

Affiliations

  • 1 Microbiology Unit, Nuclear Medical Applications, Belgian Nuclear Research Centre (SCK CEN), 2400 Mol, Belgium; Center for Microbial Ecology and Technology (CMET), Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium.
  • 2 Microbiology Unit, Nuclear Medical Applications, Belgian Nuclear Research Centre (SCK CEN), 2400 Mol, Belgium.
  • 3 Center for Microbial Ecology and Technology (CMET), Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium; Centre for Advanced Process Technology for Urban REsource Recovery (CAPTURE), 9000 Ghent, Belgium.
  • 4 Microbiology Unit, Nuclear Medical Applications, Belgian Nuclear Research Centre (SCK CEN), 2400 Mol, Belgium. Electronic address: felice.mastroleo@sckcen.be.
PMID: 37347668 DOI: 10.1016/j.xpro.2023.102358
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.1.

Keywords

Microbiology; Molecular Biology; RNAseq.

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