Assessing and reducing sources of gene expression variability in Staphylococcus epidermidis biofilms
Autor(a) principal: | |
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Data de Publicação: | 2014 |
Outros Autores: | , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
Texto Completo: | http://hdl.handle.net/1822/31922 |
Resumo: | 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. |
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Assessing and reducing sources of gene expression variability in Staphylococcus epidermidis biofilmsbiofilmsgene expression variabilitybiofilm poolRNA extractionreverse transcriptaseqPCRScience & TechnologyGene 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.We would like to thank Kimberly K. Jefferson at Virginia Commonwealth University for reviewing the manuscript. This work was co-funded by Fundacao para a Ciencia e a Tecno logia (FCT) and COMPETE grants PTDC/BIA-MIC/113450/2009 and FCOMP-01-0124-FEDER-014309, FCT Strategic Project PEst-OE/EQB/LA0023/2013, and FCT project RECI/BBB-EBI/0179/2012 (FCOMP-01-0124-FEDER-027462), and by OREN, FEDER, ON2 project. NORTE-07-0124-FEDER-000027. N.C. is an Investigador FCT.Eaton Publishing CompanyUniversidade do MinhoSousa, CármenFrança, ÂngelaCerca, Nuno2014-122014-12-01T00:00:00Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleapplication/pdfhttp://hdl.handle.net/1822/31922engSousa, Cármen; França, Ângela; Cerca, Nuno, Assessing and reducing sources of gene expression variability in S. epidermidis biofilms. BioTechniques, 57(6), 295-301, 20140736-620510.2144/00011423825495729http://www.biotechniques.cominfo:eu-repo/semantics/openAccessreponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãoinstacron:RCAAP2023-07-21T12:33:40Zoai:repositorium.sdum.uminho.pt:1822/31922Portal AgregadorONGhttps://www.rcaap.pt/oai/openaireopendoar:71602024-03-19T19:29:13.618102Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãofalse |
dc.title.none.fl_str_mv |
Assessing and reducing sources of gene expression variability in Staphylococcus epidermidis biofilms |
title |
Assessing and reducing sources of gene expression variability in Staphylococcus epidermidis biofilms |
spellingShingle |
Assessing and reducing sources of gene expression variability in Staphylococcus epidermidis biofilms Sousa, Cármen biofilms gene expression variability biofilm pool RNA extraction reverse transcriptase qPCR Science & Technology |
title_short |
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_sort |
Assessing and reducing sources of gene expression variability in Staphylococcus epidermidis biofilms |
author |
Sousa, Cármen |
author_facet |
Sousa, Cármen França, Ângela Cerca, Nuno |
author_role |
author |
author2 |
França, Ângela Cerca, Nuno |
author2_role |
author author |
dc.contributor.none.fl_str_mv |
Universidade do Minho |
dc.contributor.author.fl_str_mv |
Sousa, Cármen França, Ângela Cerca, Nuno |
dc.subject.por.fl_str_mv |
biofilms gene expression variability biofilm pool RNA extraction reverse transcriptase qPCR Science & Technology |
topic |
biofilms gene expression variability biofilm pool RNA extraction reverse transcriptase qPCR Science & Technology |
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. |
publishDate |
2014 |
dc.date.none.fl_str_mv |
2014-12 2014-12-01T00:00:00Z |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/article |
format |
article |
status_str |
publishedVersion |
dc.identifier.uri.fl_str_mv |
http://hdl.handle.net/1822/31922 |
url |
http://hdl.handle.net/1822/31922 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
Sousa, Cármen; França, Ângela; Cerca, Nuno, Assessing and reducing sources of gene expression variability in S. epidermidis biofilms. BioTechniques, 57(6), 295-301, 2014 0736-6205 10.2144/000114238 25495729 http://www.biotechniques.com |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.format.none.fl_str_mv |
application/pdf |
dc.publisher.none.fl_str_mv |
Eaton Publishing Company |
publisher.none.fl_str_mv |
Eaton Publishing Company |
dc.source.none.fl_str_mv |
reponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação instacron:RCAAP |
instname_str |
Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação |
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RCAAP |
institution |
RCAAP |
reponame_str |
Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
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Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
repository.name.fl_str_mv |
Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação |
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1799132790580576256 |