Assessing and reducing sources of gene expression variability in Staphylococcus epidermidis biofilms
Gene expression quantification can be a useful tool in studying the properties of bacterial biofilms. Unfortunately, techniques such as RNA extraction, cDNA synthesis, and quantitative PCR (qPCR) can introduce variability into mRNA transcript measurements, obscuring biologically relevant results. He...
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| Format: | Article |
| Language: | English |
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Taylor & Francis Group
2014-12-01
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| Series: | BioTechniques |
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| Online Access: | https://www.future-science.com/doi/10.2144/000114238 |
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| _version_ | 1850152571642052608 |
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| author | Cármen Sousa Angela França Nuno Cerca |
| author_facet | Cármen Sousa Angela França Nuno Cerca |
| author_sort | Cármen Sousa |
| collection | DOAJ |
| description | Gene expression quantification can be a useful tool in studying the properties of bacterial biofilms. Unfortunately, techniques such as RNA extraction, cDNA synthesis, and quantitative PCR (qPCR) can introduce variability into mRNA transcript measurements, obscuring biologically relevant results. Here we sought to identify the steps that impair accurate gene expression quantification from Staphylococcus epidermidis biofilm samples. We devised an experimental setup that could be used to determine the contribution of each experimental step to the variability of mRNA transcript measurement. Among factors tested, biofilm growth contributed the most bias to gene expression quantification. Additional experiments demonstrated that pooling biofilms together reduced this variability, resulting in more accurate gene expression analysis results. We therefore recommend pooling in order to reduce the variability associated with gene expression quantification from biofilm samples. |
| format | Article |
| id | doaj-art-0e500edd11c14bb787784119bb2ff3a3 |
| institution | OA Journals |
| issn | 0736-6205 1940-9818 |
| language | English |
| publishDate | 2014-12-01 |
| publisher | Taylor & Francis Group |
| record_format | Article |
| series | BioTechniques |
| spelling | doaj-art-0e500edd11c14bb787784119bb2ff3a32025-08-20T02:25:56ZengTaylor & Francis GroupBioTechniques0736-62051940-98182014-12-0157629530110.2144/000114238Assessing and reducing sources of gene expression variability in Staphylococcus epidermidis biofilmsCármen Sousa0Angela França1Nuno Cerca21CEB—Centre of Biological Engineering, LIBRO—Laboratory of Research in Biofilms Rosário Oliveira, University of Minho, Braga, Portugal1CEB—Centre of Biological Engineering, LIBRO—Laboratory of Research in Biofilms Rosário Oliveira, University of Minho, Braga, Portugal1CEB—Centre of Biological Engineering, LIBRO—Laboratory of Research in Biofilms Rosário Oliveira, University of Minho, Braga, PortugalGene expression quantification can be a useful tool in studying the properties of bacterial biofilms. Unfortunately, techniques such as RNA extraction, cDNA synthesis, and quantitative PCR (qPCR) can introduce variability into mRNA transcript measurements, obscuring biologically relevant results. Here we sought to identify the steps that impair accurate gene expression quantification from Staphylococcus epidermidis biofilm samples. We devised an experimental setup that could be used to determine the contribution of each experimental step to the variability of mRNA transcript measurement. Among factors tested, biofilm growth contributed the most bias to gene expression quantification. Additional experiments demonstrated that pooling biofilms together reduced this variability, resulting in more accurate gene expression analysis results. We therefore recommend pooling in order to reduce the variability associated with gene expression quantification from biofilm samples.https://www.future-science.com/doi/10.2144/000114238biofilmsgene expression variabilitybiofilm poolRNA extractionreverse transcriptaseqPCR |
| spellingShingle | Cármen Sousa Angela França Nuno Cerca Assessing and reducing sources of gene expression variability in Staphylococcus epidermidis biofilms BioTechniques biofilms gene expression variability biofilm pool RNA extraction reverse transcriptase qPCR |
| title | Assessing and reducing sources of gene expression variability in Staphylococcus epidermidis biofilms |
| title_full | Assessing and reducing sources of gene expression variability in Staphylococcus epidermidis biofilms |
| title_fullStr | Assessing and reducing sources of gene expression variability in Staphylococcus epidermidis biofilms |
| title_full_unstemmed | Assessing and reducing sources of gene expression variability in Staphylococcus epidermidis biofilms |
| title_short | Assessing and reducing sources of gene expression variability in Staphylococcus epidermidis biofilms |
| title_sort | assessing and reducing sources of gene expression variability in staphylococcus epidermidis biofilms |
| topic | biofilms gene expression variability biofilm pool RNA extraction reverse transcriptase qPCR |
| url | https://www.future-science.com/doi/10.2144/000114238 |
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