Transcriptome analysis in non-model species: a new method for the analysis of heterologous hybridization on microarrays
<p>Abstract</p> <p>Background</p> <p>Recent developments in high-throughput methods of analyzing transcriptomic profiles are promising for many areas of biology, including ecophysiology. However, although commercial microarrays are available for most common laboratory m...
| Main Authors: | , , , , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2010-05-01
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| Series: | BMC Genomics |
| Online Access: | http://www.biomedcentral.com/1471-2164/11/344 |
| _version_ | 1811320459480793088 |
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| author | Jouventin Pierre Chuchana Paul Forcheron Fabien de Dinechin Marc Rey Benjamin Keime Céline Degletagne Cyril Gautier Christian Duchamp Claude |
| author_facet | Jouventin Pierre Chuchana Paul Forcheron Fabien de Dinechin Marc Rey Benjamin Keime Céline Degletagne Cyril Gautier Christian Duchamp Claude |
| author_sort | Jouventin Pierre |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>Recent developments in high-throughput methods of analyzing transcriptomic profiles are promising for many areas of biology, including ecophysiology. However, although commercial microarrays are available for most common laboratory models, transcriptome analysis in non-traditional model species still remains a challenge. Indeed, the signal resulting from heterologous hybridization is low and difficult to interpret because of the weak complementarity between probe and target sequences, especially when no microarray dedicated to a genetically close species is available.</p> <p>Results</p> <p>We show here that transcriptome analysis in a species genetically distant from laboratory models is made possible by using <smcaps>MAXRS</smcaps>, a new method of analyzing heterologous hybridization on microarrays. This method takes advantage of the design of several commercial microarrays, with different probes targeting the same transcript. To illustrate and test this method, we analyzed the transcriptome of king penguin pectoralis muscle hybridized to Affymetrix chicken microarrays, two organisms separated by an evolutionary distance of approximately 100 million years. The differential gene expression observed between different physiological situations computed by <smcaps>MAXRS</smcaps> was confirmed by real-time PCR on 10 genes out of 11 tested.</p> <p>Conclusions</p> <p><smcaps>MAXRS</smcaps> appears to be an appropriate method for gene expression analysis under heterologous hybridization conditions.</p> |
| first_indexed | 2024-04-13T12:59:42Z |
| format | Article |
| id | doaj.art-94a9545fcdd441d7acf03e9e284c0e2c |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-04-13T12:59:42Z |
| publishDate | 2010-05-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-94a9545fcdd441d7acf03e9e284c0e2c2022-12-22T02:45:57ZengBMCBMC Genomics1471-21642010-05-0111134410.1186/1471-2164-11-344Transcriptome analysis in non-model species: a new method for the analysis of heterologous hybridization on microarraysJouventin PierreChuchana PaulForcheron Fabiende Dinechin MarcRey BenjaminKeime CélineDegletagne CyrilGautier ChristianDuchamp Claude<p>Abstract</p> <p>Background</p> <p>Recent developments in high-throughput methods of analyzing transcriptomic profiles are promising for many areas of biology, including ecophysiology. However, although commercial microarrays are available for most common laboratory models, transcriptome analysis in non-traditional model species still remains a challenge. Indeed, the signal resulting from heterologous hybridization is low and difficult to interpret because of the weak complementarity between probe and target sequences, especially when no microarray dedicated to a genetically close species is available.</p> <p>Results</p> <p>We show here that transcriptome analysis in a species genetically distant from laboratory models is made possible by using <smcaps>MAXRS</smcaps>, a new method of analyzing heterologous hybridization on microarrays. This method takes advantage of the design of several commercial microarrays, with different probes targeting the same transcript. To illustrate and test this method, we analyzed the transcriptome of king penguin pectoralis muscle hybridized to Affymetrix chicken microarrays, two organisms separated by an evolutionary distance of approximately 100 million years. The differential gene expression observed between different physiological situations computed by <smcaps>MAXRS</smcaps> was confirmed by real-time PCR on 10 genes out of 11 tested.</p> <p>Conclusions</p> <p><smcaps>MAXRS</smcaps> appears to be an appropriate method for gene expression analysis under heterologous hybridization conditions.</p>http://www.biomedcentral.com/1471-2164/11/344 |
| spellingShingle | Jouventin Pierre Chuchana Paul Forcheron Fabien de Dinechin Marc Rey Benjamin Keime Céline Degletagne Cyril Gautier Christian Duchamp Claude Transcriptome analysis in non-model species: a new method for the analysis of heterologous hybridization on microarrays BMC Genomics |
| title | Transcriptome analysis in non-model species: a new method for the analysis of heterologous hybridization on microarrays |
| title_full | Transcriptome analysis in non-model species: a new method for the analysis of heterologous hybridization on microarrays |
| title_fullStr | Transcriptome analysis in non-model species: a new method for the analysis of heterologous hybridization on microarrays |
| title_full_unstemmed | Transcriptome analysis in non-model species: a new method for the analysis of heterologous hybridization on microarrays |
| title_short | Transcriptome analysis in non-model species: a new method for the analysis of heterologous hybridization on microarrays |
| title_sort | transcriptome analysis in non model species a new method for the analysis of heterologous hybridization on microarrays |
| url | http://www.biomedcentral.com/1471-2164/11/344 |
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