RNA extraction protocol from low-biomass bacterial Nitrosomonas europaea and Nitrobacter winogradskyi cultures for whole transcriptome studies.
| Autor: | Verbeelen T; 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., Van Houdt R; Microbiology Unit, Nuclear Medical Applications, Belgian Nuclear Research Centre (SCK CEN), 2400 Mol, Belgium., Leys N; Microbiology Unit, Nuclear Medical Applications, Belgian Nuclear Research Centre (SCK CEN), 2400 Mol, Belgium., Ganigué R; 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., Mastroleo F; Microbiology Unit, Nuclear Medical Applications, Belgian Nuclear Research Centre (SCK CEN), 2400 Mol, Belgium. Electronic address: felice.mastroleo@sckcen.be. |
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| Jazyk: | angličtina |
| Zdroj: | STAR protocols [STAR Protoc] 2023 Sep 15; Vol. 4 (3), pp. 102358. Date of Electronic Publication: 2023 Jun 21. |
| DOI: | 10.1016/j.xpro.2023.102358 |
| Abstrakt: | 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 . Competing Interests: Declaration of interests The authors declare no competing interests. (Copyright © 2023 The Authors. Published by Elsevier Inc. All rights reserved.) |
| Databáze: | MEDLINE |
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