Reference genes for quantitative RT-PCR data in gastric tissues and cell lines
Autor(a) principal: | |
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Data de Publicação: | 2013 |
Outros Autores: | , , , , , , , , , , |
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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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 |
_version_ |
1814268450055389184 |