Open Access Highly Accessed Methodology article

Transcriptome analysis in non-model species: a new method for the analysis of heterologous hybridization on microarrays

Cyril Degletagne1, Céline Keime2*, Benjamin Rey3, Marc de Dinechin45, Fabien Forcheron1, Paul Chuchana67, Pierre Jouventin4, Christian Gautier2 and Claude Duchamp1

  • * Corresponding author: Céline Keime keime@prabi.fr

  • † Equal contributors

Author Affiliations

1 Université de Lyon, F-69000, Lyon; Laboratoire de Physiologie Intégrative, Cellulaire et Moléculaire, UMR 5123 CNRS - Université Lyon 1, 43 Bvd 11 Novembre 1918, F-69622 Villeurbanne Cedex, France

2 Pôle Rhône Alpes de Bioinformatique, Université Lyon 1, Bâtiment Gregor Mendel, 16 rue Raphaël Dubois, 69622 Villeurbanne cedex, France

3 Université de Lyon, F-69000, Lyon; Laboratoire de Biométrie et Biologie Evolutive, UMR 5558 CNRS - Université Lyon 1, 43 Bvd 11 Novembre 1918, F-69622 Villeurbanne Cedex, France

4 UMR 5175 Centre d'Ecologie Fonctionnelle et Evolutive - CNRS, 1919 route de Mende 34293 Montpellier CEDEX 5, France

5 UMR 2724 Génétique et Évolution des Maladies Infectieuses - CNRS-IRD, 911 avenue Agropolis, 34394 Montpellier Cedex 5, France

6 CIRAD UMR 17 [UMR 177 IRD-CIRAD], TA A-17/G, Campus International de Baillarguet, 34398 Montpellier CEDEX 5, France

7 U844, 80 avenue Augustin Fliche F-34295 Montpellier, France

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BMC Genomics 2010, 11:344  doi:10.1186/1471-2164-11-344

Published: 31 May 2010

Additional files

Additional file 1:

Penguin and chicken orthologous sequences. GenBank accession numbers of penguin sequences together with the accession numbers of their orthologous chicken sequences, the corresponding Hovergen family identification number and the percent identity between each pair of sequences.

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Additional file 2:

Comparison of the gene expression differences between qPCR using primers designed against chicken and against penguin transcript sequences. Expression fold changes of the six genes tested by quantitative PCR using primers designed against chicken (black bars) vs. penguin sequences (gray bars). These fold changes correspond to SA/NI for the genes up-regulated during the transition from terrestrial to marine life (represented above the x-axis) and to NI/SA for the down-regulated genes (represented below the x-axis).

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Additional file 3:

Comparison of the gene expression differences assessed by GCOS analysis and by qPCR. Expression fold changes of the six differentially expressed genes determined with GCOS and with qPCR. These fold changes correspond to SA/NI for the genes up-regulated during the transition from terrestrial to marine life (represented above the x-axis) and to NI/SA for the down-regulated genes (represented below the x-axis). The white bars correspond to the fold changes assessed by microarray and analyzed with GCOS, and the black bars correspond to the fold changes assessed by quantitative PCR.

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Additional file 4:

Mean intensity value and rank of each probe with an intensity above background. This file provides, for each Affymetrix probe above background, the mean intensity value and rank.

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Additional file 5:

Primer sequences used for qPCR. This file provides, for each tested gene, the corresponding Affymetrix probe set ID, the primer sequences used for qPCR and the fold changes and p-values from the microarray and qPCR.

Format: XLS Size: 27KB Download file

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