Development of an oligo DNA microarray for the European sea bass and its application to expression profiling of jaw deformity
Autor(a) principal: | |
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Data de Publicação: | 2010 |
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/10400.1/206 |
Resumo: | Abstract Background The European sea bass (Dicentrarchus labrax) is a marine fish of great importance for fisheries and aquaculture. Functional genomics offers the possibility to discover the molecular mechanisms underlying productive traits in farmed fish, and a step towards the application of marker assisted selection methods in this species. To this end, we report here on the development of an oligo DNA microarray for D. labrax. Results A database consisting of 19,048 unique transcripts was constructed, of which 12,008 (63%) could be annotated by similarity and 4,692 received a GO functional annotation. Two non-overlapping 60mer probes were designed for each unique transcript and in-situ synthesized on glass slides using Agilent SurePrint™ technology. Probe design was positively completed for 19,035 target clusters; the oligo microarray was then applied to profile gene expression in mandibles and whole-heads of fish affected by prognathism, a skeletal malformation that strongly affects sea bass production. Statistical analysis identified 242 transcripts that are significantly down-regulated in deformed individuals compared to normal fish, with a significant enrichment in genes related to nervous system development and functioning. A set of genes spanning a wide dynamic range in gene expression level were selected for quantitative RT-PCR validation. Fold change correlation between microarray and qPCR data was always significant. Conclusions The microarray platform developed for the European sea bass has a high level of flexibility, reliability, and reproducibility. Despite the well known limitations in achieving a proper functional annotation in non-model species, sufficient information was obtained to identify biological processes that are significantly enriched among differentially expressed genes. New insights were obtained on putative mechanisms involved on mandibular prognathism, suggesting that bone/nervous system development might play a role in this phenomenon. |
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Development of an oligo DNA microarray for the European sea bass and its application to expression profiling of jaw deformityAbstract Background The European sea bass (Dicentrarchus labrax) is a marine fish of great importance for fisheries and aquaculture. Functional genomics offers the possibility to discover the molecular mechanisms underlying productive traits in farmed fish, and a step towards the application of marker assisted selection methods in this species. To this end, we report here on the development of an oligo DNA microarray for D. labrax. Results A database consisting of 19,048 unique transcripts was constructed, of which 12,008 (63%) could be annotated by similarity and 4,692 received a GO functional annotation. Two non-overlapping 60mer probes were designed for each unique transcript and in-situ synthesized on glass slides using Agilent SurePrint™ technology. Probe design was positively completed for 19,035 target clusters; the oligo microarray was then applied to profile gene expression in mandibles and whole-heads of fish affected by prognathism, a skeletal malformation that strongly affects sea bass production. Statistical analysis identified 242 transcripts that are significantly down-regulated in deformed individuals compared to normal fish, with a significant enrichment in genes related to nervous system development and functioning. A set of genes spanning a wide dynamic range in gene expression level were selected for quantitative RT-PCR validation. Fold change correlation between microarray and qPCR data was always significant. Conclusions The microarray platform developed for the European sea bass has a high level of flexibility, reliability, and reproducibility. Despite the well known limitations in achieving a proper functional annotation in non-model species, sufficient information was obtained to identify biological processes that are significantly enriched among differentially expressed genes. New insights were obtained on putative mechanisms involved on mandibular prognathism, suggesting that bone/nervous system development might play a role in this phenomenon.SapientiaFerraresso, SerenaMilan, MassimoPellizzari, CaterinaVitulo, NicolaReinhardt, RichardCanario, Adelino V. M.Patarnello, T.Bargelloni, Luca2011-06-03T10:03:37Z2010-06-032011-06-03T10:03:38Z2010-06-03T00:00:00Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articletext/xmlapplication/vnd.openxmlformats-officedocument.spreadsheetml.sheetapplication/vnd.ms-excelapplication/pdfapplication/pdfapplication/pdfapplication/mswordapplication/mswordapplication/pdfhttp://hdl.handle.net/10400.1/206engBMC Genomics. 2010 Jun 03;11(1):354AUT: ACA00258;http://dx.doi.org/10.1186/1471-2164-11-354info: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:RCAAP2023-07-24T10:10:56Zoai:sapientia.ualg.pt:10400.1/206Portal AgregadorONGhttps://www.rcaap.pt/oai/openaireopendoar:71602024-03-19T19:54:36.376614Repositório 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 |
Development of an oligo DNA microarray for the European sea bass and its application to expression profiling of jaw deformity |
title |
Development of an oligo DNA microarray for the European sea bass and its application to expression profiling of jaw deformity |
spellingShingle |
Development of an oligo DNA microarray for the European sea bass and its application to expression profiling of jaw deformity Ferraresso, Serena |
title_short |
Development of an oligo DNA microarray for the European sea bass and its application to expression profiling of jaw deformity |
title_full |
Development of an oligo DNA microarray for the European sea bass and its application to expression profiling of jaw deformity |
title_fullStr |
Development of an oligo DNA microarray for the European sea bass and its application to expression profiling of jaw deformity |
title_full_unstemmed |
Development of an oligo DNA microarray for the European sea bass and its application to expression profiling of jaw deformity |
title_sort |
Development of an oligo DNA microarray for the European sea bass and its application to expression profiling of jaw deformity |
author |
Ferraresso, Serena |
author_facet |
Ferraresso, Serena Milan, Massimo Pellizzari, Caterina Vitulo, Nicola Reinhardt, Richard Canario, Adelino V. M. Patarnello, T. Bargelloni, Luca |
author_role |
author |
author2 |
Milan, Massimo Pellizzari, Caterina Vitulo, Nicola Reinhardt, Richard Canario, Adelino V. M. Patarnello, T. Bargelloni, Luca |
author2_role |
author author author author author author author |
dc.contributor.none.fl_str_mv |
Sapientia |
dc.contributor.author.fl_str_mv |
Ferraresso, Serena Milan, Massimo Pellizzari, Caterina Vitulo, Nicola Reinhardt, Richard Canario, Adelino V. M. Patarnello, T. Bargelloni, Luca |
description |
Abstract Background The European sea bass (Dicentrarchus labrax) is a marine fish of great importance for fisheries and aquaculture. Functional genomics offers the possibility to discover the molecular mechanisms underlying productive traits in farmed fish, and a step towards the application of marker assisted selection methods in this species. To this end, we report here on the development of an oligo DNA microarray for D. labrax. Results A database consisting of 19,048 unique transcripts was constructed, of which 12,008 (63%) could be annotated by similarity and 4,692 received a GO functional annotation. Two non-overlapping 60mer probes were designed for each unique transcript and in-situ synthesized on glass slides using Agilent SurePrint™ technology. Probe design was positively completed for 19,035 target clusters; the oligo microarray was then applied to profile gene expression in mandibles and whole-heads of fish affected by prognathism, a skeletal malformation that strongly affects sea bass production. Statistical analysis identified 242 transcripts that are significantly down-regulated in deformed individuals compared to normal fish, with a significant enrichment in genes related to nervous system development and functioning. A set of genes spanning a wide dynamic range in gene expression level were selected for quantitative RT-PCR validation. Fold change correlation between microarray and qPCR data was always significant. Conclusions The microarray platform developed for the European sea bass has a high level of flexibility, reliability, and reproducibility. Despite the well known limitations in achieving a proper functional annotation in non-model species, sufficient information was obtained to identify biological processes that are significantly enriched among differentially expressed genes. New insights were obtained on putative mechanisms involved on mandibular prognathism, suggesting that bone/nervous system development might play a role in this phenomenon. |
publishDate |
2010 |
dc.date.none.fl_str_mv |
2010-06-03 2010-06-03T00:00:00Z 2011-06-03T10:03:37Z 2011-06-03T10:03:38Z |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/article |
format |
article |
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publishedVersion |
dc.identifier.uri.fl_str_mv |
http://hdl.handle.net/10400.1/206 |
url |
http://hdl.handle.net/10400.1/206 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
BMC Genomics. 2010 Jun 03;11(1):354 AUT: ACA00258; http://dx.doi.org/10.1186/1471-2164-11-354 |
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info:eu-repo/semantics/openAccess |
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openAccess |
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Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação |
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RCAAP |
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Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
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Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
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Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação |
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