Identification and validation of reference genes in Clostridium beijerinckii NRRL B-598 for RT-qPCR using RNA-Seq data

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dc.contributor.authorŠabatová, Kateřinacs
dc.contributor.authorRaschmanová, Hanacs
dc.contributor.authorKolek, Jancs
dc.contributor.authorVasylkivska, Marynacs
dc.contributor.authorBranská, Barboracs
dc.contributor.authorPatáková, Petracs
dc.contributor.authorProvazník, Valentýnacs
dc.contributor.authorSedlář, Karelcs
dc.coverage.issue1cs
dc.coverage.volume12cs
dc.date.issued2021-03-04cs
dc.description.abstractGene expression analysis through reverse transcription-quantitative real-time polymerase chain reaction (RT-qPCR) depends on correct data normalization by reference genes with stable expression. Although Clostridium beijerinckii NRRL B-598 is a promising Gram-positive bacterium for the industrial production of biobutanol, validated reference genes have not yet been reported. In this study, we selected 160 genes with stable expression based on an RNA sequencing (RNA-Seq) data analysis, and among them, seven genes (zmp, rpoB1, rsmB, greA, rpoB2, topB2, and rimO) were selected for experimental validation by RT-qPCR and gene ontology enrichment analysis. According to statistical analyses, zmp and greA were the most stable and suitable reference genes for RT-qPCR normalization. Furthermore, our methodology can be useful for selection of the reference genes in other strains of Clostridium beijerinckii and it also suggests that the RNA-Seq data can be used for the initial selection of novel reference genes, however their validation is required.en
dc.formattextcs
dc.format.extent1-10cs
dc.format.mimetypeapplication/pdfcs
dc.identifier.citationFrontiers in Microbiology. 2021, vol. 12, issue 1, p. 1-10.en
dc.identifier.doi10.3389/fmicb.2021.640054cs
dc.identifier.issn1664-302Xcs
dc.identifier.orcid0000-0001-5143-9521cs
dc.identifier.orcid0000-0002-3422-7938cs
dc.identifier.orcid0000-0002-8269-4020cs
dc.identifier.other169963cs
dc.identifier.researcheridAAC-2736-2019cs
dc.identifier.researcheridF-4121-2012cs
dc.identifier.researcheridK-1120-2014cs
dc.identifier.scopus57205673155cs
dc.identifier.scopus6701729526cs
dc.identifier.scopus56309904900cs
dc.identifier.urihttp://hdl.handle.net/11012/196506
dc.language.isoencs
dc.publisherFrontierscs
dc.relation.ispartofFrontiers in Microbiologycs
dc.relation.urihttps://www.frontiersin.org/articles/10.3389/fmicb.2021.640054/fullcs
dc.rightsCreative Commons Attribution 4.0 Internationalcs
dc.rights.accessopenAccesscs
dc.rights.sherpahttp://www.sherpa.ac.uk/romeo/issn/1664-302X/cs
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/cs
dc.subjectHKGen
dc.subjecthousekeeping genesen
dc.subjectnon-model organismsen
dc.subjectbiofuelen
dc.subjectClostridiumen
dc.titleIdentification and validation of reference genes in Clostridium beijerinckii NRRL B-598 for RT-qPCR using RNA-Seq dataen
dc.type.driverarticleen
dc.type.statusPeer-revieweden
dc.type.versionpublishedVersionen
sync.item.dbidVAV-169963en
sync.item.dbtypeVAVen
sync.item.insts2025.02.03 15:39:46en
sync.item.modts2025.01.17 16:34:18en
thesis.grantorVysoké učení technické v Brně. Fakulta elektrotechniky a komunikačních technologií. Ústav biomedicínského inženýrstvícs
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