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Open Access Research article

A pig multi-tissue normalised cDNA library: large-scale sequencing, cluster analysis and 9K micro-array resource generation

Agnès Bonnet1, Eddie Iannuccelli2, Karine Hugot34, Francis Benne1, Maria F Bonaldo5, Marcelo B Soares5, François Hatey1 and Gwenola Tosser-Klopp1*

Author Affiliations

1 Laboratoire de Génétique Cellulaire, INRA, UMR444, Institut National de la Recherche Agronomique, F-31326 Castanet-Tolosan, France

2 Sigenae, INRA, Institut National de la Recherche Agronomique, F-31326 Castanet-Tolosan, France

3 Laboratoire de Radiobiologie et d'Etude du Génome, UMR314, INRA, CRB GADIE, Institut National de la Recherche Agronomique, F-78352 Jouy-en-Josas, France

4 Laboratoire de Radiobiologie et d'Etude du Génome, CEA, DSV, IRCM, Commissariat à l'Energie Atomique, F-78352 Jouy-en-Josas, France

5 Children's Memorial Research Center, Northwestern University's Feinberg School of Medicine, Chicago, IL, USA

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BMC Genomics 2008, 9:17  doi:10.1186/1471-2164-9-17

Published: 14 January 2008

Abstract

Background

Domestic animal breeding and product quality improvement require the control of reproduction, nutrition, health and welfare in these animals. It is thus necessary to improve our knowledge of the major physiological functions and their interactions. This would be greatly enhanced by the availability of expressed gene sequences in the databases and by cDNA arrays allowing the transcriptome analysis of any function.

The objective within the AGENAE French program was to initiate a high-throughput cDNA sequencing program of a 38-tissue normalised library and generate a diverse microarray for transcriptome analysis in pig species.

Results

We constructed a multi-tissue cDNA library, which was normalised and subtracted to reduce the redundancy of the clones. Expressed Sequence Tags were produced and 24449 high-quality sequences were released in EMBL database. The assembly of all the public ESTs (available through SIGENAE website) resulted in 40786 contigs and 54653 singletons. At least one Agenae sequence is present in 11969 contigs (12.5%) and in 9291 of the deeper-than-one-contigs (22.8%). Sequence analysis showed that both normalisation and subtraction processes were successful and that the initial tissue complexity was maintained in the final libraries. A 9K nylon cDNA microarray was produced and is available through CRB-GADIE. It will allow high sensitivity transcriptome analyses in pigs.

Conclusion

In the present work, a pig multi-tissue cDNA library was constructed and a 9K cDNA microarray designed. It contributes to the Expressed Sequence Tags pig data, and offers a valuable tool for transcriptome analysis.