Reference genes for quantitative RT-PCR data in gastric tissues and cell lines

Detalhes bibliográficos
Autor(a) principal: Wisnieski, Fernanda [UNIFESP]
Data de Publicação: 2013
Outros Autores: Calcagno, Danielle Queiroz [UNIFESP], Leal, Mariana Ferreira [UNIFESP], Santos, Leonardo Caires dos [UNIFESP], Gigek, Carolina Oliveira [UNIFESP], Chen, Elizabeth Suchi [UNIFESP], Pontes, Thais Brilhante [UNIFESP], Assumpção, Paulo Pimentel [UNIFESP], Assumpção, Mônica Barauna de [UNIFESP], Demachki, Samia, Burbano, Rommel Rodriguez, Smith, Marilia de Arruda Cardoso
Tipo de documento: Artigo
Idioma: eng
Título da fonte: Repositório Institucional da UNIFESP
Texto Completo: http://dx.doi.org/10.3748/wjg.v19.i41.7121
http://repositorio.unifesp.br/handle/11600/36973
Resumo: AIM: To evaluate the suitability of reference genes in gastric tissue samples and cell lines.METHODS: the suitability of genes ACTB, B2M, GAPDH, RPL29, and 18S rRNA was assessed in 21 matched pairs of neoplastic and adjacent nonneoplastic gastric tissues from patients with gastric adenocarcinoma, 27 normal gastric tissues from patients without cancer, and 4 cell lines using reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR). the ranking of the best single and combination of reference genes was determined by NormFinder, geNorm (TM), BestKeeper, and DataAssist (TM). in addition, GenEx software was used to determine the optimal number of reference genes. To validate the results, the mRNA expression of a target gene, DNMT1, was quantified using the different reference gene combinations suggested by the various software packages for normalization.RESULTS: ACTB was the best reference gene for all gastric tissues, cell lines and all gastric tissues plus cell lines. GAPDH + B2M or ACTB + B2M was the best combination of reference genes for all the gastric tissues. On the other hand, ACTB + B2M was the best combination for all the cell lines tested and was also the best combination for analyses involving all the gastric tissues plus cell lines. According to the GenEx software, 2 or 3 genes were the optimal number of references genes for all the gastric tissues. the relative quantification of DNMT1 showed similar patterns when normalized by each combination of reference genes. the level of expression of DNMT1 in neoplastic, adjacent non-neoplastic and normal gastric tissues did not differ when these samples were normalized using GAPDH + B2M (P = 0.32), ACTB + B2M (P = 0.61), or GAPDH + B2M + ACTB (P = 0.44).CONCLUSION: GAPDH + B2M or ACTB + B2M is the best combination of reference gene for all the gastric tissues, and ACTB + B2M is the best combination for the cell lines tested. (C) 2013 Baishideng Publishing Group Co., Limited. All rights reserved.
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spelling Reference genes for quantitative RT-PCR data in gastric tissues and cell linesGastric cancerReference geneNormalizationGene expressionQuantitative real-time polymerase chain reactionAIM: To evaluate the suitability of reference genes in gastric tissue samples and cell lines.METHODS: the suitability of genes ACTB, B2M, GAPDH, RPL29, and 18S rRNA was assessed in 21 matched pairs of neoplastic and adjacent nonneoplastic gastric tissues from patients with gastric adenocarcinoma, 27 normal gastric tissues from patients without cancer, and 4 cell lines using reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR). the ranking of the best single and combination of reference genes was determined by NormFinder, geNorm (TM), BestKeeper, and DataAssist (TM). in addition, GenEx software was used to determine the optimal number of reference genes. To validate the results, the mRNA expression of a target gene, DNMT1, was quantified using the different reference gene combinations suggested by the various software packages for normalization.RESULTS: ACTB was the best reference gene for all gastric tissues, cell lines and all gastric tissues plus cell lines. GAPDH + B2M or ACTB + B2M was the best combination of reference genes for all the gastric tissues. On the other hand, ACTB + B2M was the best combination for all the cell lines tested and was also the best combination for analyses involving all the gastric tissues plus cell lines. According to the GenEx software, 2 or 3 genes were the optimal number of references genes for all the gastric tissues. the relative quantification of DNMT1 showed similar patterns when normalized by each combination of reference genes. the level of expression of DNMT1 in neoplastic, adjacent non-neoplastic and normal gastric tissues did not differ when these samples were normalized using GAPDH + B2M (P = 0.32), ACTB + B2M (P = 0.61), or GAPDH + B2M + ACTB (P = 0.44).CONCLUSION: GAPDH + B2M or ACTB + B2M is the best combination of reference gene for all the gastric tissues, and ACTB + B2M is the best combination for the cell lines tested. (C) 2013 Baishideng Publishing Group Co., Limited. All rights reserved.Universidade Federal de São Paulo, Dept Morfol & Genet, Disciplina Genet, BR-04023900 São Paulo, BrazilUniversidade Federal de São Paulo, Dept Ortopedia & Traumatol, BR-04038031 São Paulo, BrazilFed Univ Para, Nucleo Pesquisa Oncol, Hosp Joao de Barros Barreto, BR-60673000 Belem, Para, BrazilFed Univ Para, Lab Citogenet Humana, Inst Ciencias Biol, BR-66075110 Belem, Para, BrazilUniversidade Federal de São Paulo, Dept Morfol & Genet, Disciplina Genet, BR-04023900 São Paulo, BrazilUniversidade Federal de São Paulo, Dept Ortopedia & Traumatol, BR-04038031 São Paulo, BrazilWeb of ScienceCoordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Baishideng Publishing Group IncUniversidade Federal de São Paulo (UNIFESP)Fed Univ ParaWisnieski, Fernanda [UNIFESP]Calcagno, Danielle Queiroz [UNIFESP]Leal, Mariana Ferreira [UNIFESP]Santos, Leonardo Caires dos [UNIFESP]Gigek, Carolina Oliveira [UNIFESP]Chen, Elizabeth Suchi [UNIFESP]Pontes, Thais Brilhante [UNIFESP]Assumpção, Paulo Pimentel [UNIFESP]Assumpção, Mônica Barauna de [UNIFESP]Demachki, SamiaBurbano, Rommel RodriguezSmith, Marilia de Arruda Cardoso2016-01-24T14:34:42Z2016-01-24T14:34:42Z2013-11-07info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersion7121-7128http://dx.doi.org/10.3748/wjg.v19.i41.7121World Journal of Gastroenterology. Pleasanton: Baishideng Publishing Group Inc, v. 19, n. 41, p. 7121-7128, 2013.10.3748/wjg.v19.i41.71211007-9327http://repositorio.unifesp.br/handle/11600/36973WOS:000327068400019engWorld Journal of Gastroenterologyinfo:eu-repo/semantics/openAccessreponame:Repositório Institucional da UNIFESPinstname:Universidade Federal de São Paulo (UNIFESP)instacron:UNIFESP2024-10-10T13:38:31Zoai:repositorio.unifesp.br/:11600/36973Repositório InstitucionalPUBhttp://www.repositorio.unifesp.br/oai/requestbiblioteca.csp@unifesp.bropendoar:34652024-10-10T13:38:31Repositório Institucional da UNIFESP - Universidade Federal de São Paulo (UNIFESP)false
dc.title.none.fl_str_mv Reference genes for quantitative RT-PCR data in gastric tissues and cell lines
title Reference genes for quantitative RT-PCR data in gastric tissues and cell lines
spellingShingle Reference genes for quantitative RT-PCR data in gastric tissues and cell lines
Wisnieski, Fernanda [UNIFESP]
Gastric cancer
Reference gene
Normalization
Gene expression
Quantitative real-time polymerase chain reaction
title_short Reference genes for quantitative RT-PCR data in gastric tissues and cell lines
title_full Reference genes for quantitative RT-PCR data in gastric tissues and cell lines
title_fullStr Reference genes for quantitative RT-PCR data in gastric tissues and cell lines
title_full_unstemmed Reference genes for quantitative RT-PCR data in gastric tissues and cell lines
title_sort Reference genes for quantitative RT-PCR data in gastric tissues and cell lines
author Wisnieski, Fernanda [UNIFESP]
author_facet Wisnieski, Fernanda [UNIFESP]
Calcagno, Danielle Queiroz [UNIFESP]
Leal, Mariana Ferreira [UNIFESP]
Santos, Leonardo Caires dos [UNIFESP]
Gigek, Carolina Oliveira [UNIFESP]
Chen, Elizabeth Suchi [UNIFESP]
Pontes, Thais Brilhante [UNIFESP]
Assumpção, Paulo Pimentel [UNIFESP]
Assumpção, Mônica Barauna de [UNIFESP]
Demachki, Samia
Burbano, Rommel Rodriguez
Smith, Marilia de Arruda Cardoso
author_role author
author2 Calcagno, Danielle Queiroz [UNIFESP]
Leal, Mariana Ferreira [UNIFESP]
Santos, Leonardo Caires dos [UNIFESP]
Gigek, Carolina Oliveira [UNIFESP]
Chen, Elizabeth Suchi [UNIFESP]
Pontes, Thais Brilhante [UNIFESP]
Assumpção, Paulo Pimentel [UNIFESP]
Assumpção, Mônica Barauna de [UNIFESP]
Demachki, Samia
Burbano, Rommel Rodriguez
Smith, Marilia de Arruda Cardoso
author2_role author
author
author
author
author
author
author
author
author
author
author
dc.contributor.none.fl_str_mv Universidade Federal de São Paulo (UNIFESP)
Fed Univ Para
dc.contributor.author.fl_str_mv Wisnieski, Fernanda [UNIFESP]
Calcagno, Danielle Queiroz [UNIFESP]
Leal, Mariana Ferreira [UNIFESP]
Santos, Leonardo Caires dos [UNIFESP]
Gigek, Carolina Oliveira [UNIFESP]
Chen, Elizabeth Suchi [UNIFESP]
Pontes, Thais Brilhante [UNIFESP]
Assumpção, Paulo Pimentel [UNIFESP]
Assumpção, Mônica Barauna de [UNIFESP]
Demachki, Samia
Burbano, Rommel Rodriguez
Smith, Marilia de Arruda Cardoso
dc.subject.por.fl_str_mv Gastric cancer
Reference gene
Normalization
Gene expression
Quantitative real-time polymerase chain reaction
topic Gastric cancer
Reference gene
Normalization
Gene expression
Quantitative real-time polymerase chain reaction
description AIM: To evaluate the suitability of reference genes in gastric tissue samples and cell lines.METHODS: the suitability of genes ACTB, B2M, GAPDH, RPL29, and 18S rRNA was assessed in 21 matched pairs of neoplastic and adjacent nonneoplastic gastric tissues from patients with gastric adenocarcinoma, 27 normal gastric tissues from patients without cancer, and 4 cell lines using reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR). the ranking of the best single and combination of reference genes was determined by NormFinder, geNorm (TM), BestKeeper, and DataAssist (TM). in addition, GenEx software was used to determine the optimal number of reference genes. To validate the results, the mRNA expression of a target gene, DNMT1, was quantified using the different reference gene combinations suggested by the various software packages for normalization.RESULTS: ACTB was the best reference gene for all gastric tissues, cell lines and all gastric tissues plus cell lines. GAPDH + B2M or ACTB + B2M was the best combination of reference genes for all the gastric tissues. On the other hand, ACTB + B2M was the best combination for all the cell lines tested and was also the best combination for analyses involving all the gastric tissues plus cell lines. According to the GenEx software, 2 or 3 genes were the optimal number of references genes for all the gastric tissues. the relative quantification of DNMT1 showed similar patterns when normalized by each combination of reference genes. the level of expression of DNMT1 in neoplastic, adjacent non-neoplastic and normal gastric tissues did not differ when these samples were normalized using GAPDH + B2M (P = 0.32), ACTB + B2M (P = 0.61), or GAPDH + B2M + ACTB (P = 0.44).CONCLUSION: GAPDH + B2M or ACTB + B2M is the best combination of reference gene for all the gastric tissues, and ACTB + B2M is the best combination for the cell lines tested. (C) 2013 Baishideng Publishing Group Co., Limited. All rights reserved.
publishDate 2013
dc.date.none.fl_str_mv 2013-11-07
2016-01-24T14:34:42Z
2016-01-24T14:34:42Z
dc.type.driver.fl_str_mv info:eu-repo/semantics/article
dc.type.status.fl_str_mv info:eu-repo/semantics/publishedVersion
format article
status_str publishedVersion
dc.identifier.uri.fl_str_mv http://dx.doi.org/10.3748/wjg.v19.i41.7121
World Journal of Gastroenterology. Pleasanton: Baishideng Publishing Group Inc, v. 19, n. 41, p. 7121-7128, 2013.
10.3748/wjg.v19.i41.7121
1007-9327
http://repositorio.unifesp.br/handle/11600/36973
WOS:000327068400019
url http://dx.doi.org/10.3748/wjg.v19.i41.7121
http://repositorio.unifesp.br/handle/11600/36973
identifier_str_mv World Journal of Gastroenterology. Pleasanton: Baishideng Publishing Group Inc, v. 19, n. 41, p. 7121-7128, 2013.
10.3748/wjg.v19.i41.7121
1007-9327
WOS:000327068400019
dc.language.iso.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv World Journal of Gastroenterology
dc.rights.driver.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv 7121-7128
dc.publisher.none.fl_str_mv Baishideng Publishing Group Inc
publisher.none.fl_str_mv Baishideng Publishing Group Inc
dc.source.none.fl_str_mv reponame:Repositório Institucional da UNIFESP
instname:Universidade Federal de São Paulo (UNIFESP)
instacron:UNIFESP
instname_str Universidade Federal de São Paulo (UNIFESP)
instacron_str UNIFESP
institution UNIFESP
reponame_str Repositório Institucional da UNIFESP
collection Repositório Institucional da UNIFESP
repository.name.fl_str_mv Repositório Institucional da UNIFESP - Universidade Federal de São Paulo (UNIFESP)
repository.mail.fl_str_mv biblioteca.csp@unifesp.br
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