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Nucleic Acids Research Advance Access published online on October 16, 2007
Nucleic Acids Research, doi:10.1093/nar/gkm757
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© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Database Issue

CATdb: a public access to Arabidopsis transcriptome data from the URGV-CATMA platform

Séverine Gagnot1, Jean-Philippe Tamby2, Marie-Laure Martin-Magniette1,3, Frédérique Bitton1, Ludivine Taconnat1, Sandrine Balzergue1, Sébastien Aubourg1, Jean-Pierre Renou1, Alain Lecharny1,4 and Véronique Brunaud1,*

1Unité de Recherche en Génomique Végétale (URGV) - UMR INRA 1165-CNRS 8114-UEVE, 2 Rue Gaston Crémieux, 91057 Evry Cedex, 2Laboratoire de Biologie Cellulaire - Institut J.P. Bourgin - INRA Centre de Versailles-Grignon, Route de Saint Cyr (RD 10), 78026 Versailles Cedex, France, 3Unité de Mathématiques et Informatique Appliquées (MIA) - UMR 518 AgroParisTech-INRA, 16 Rue Claude Bernard, 75231 Paris Cedex and 4Université Paris-Sud, Institut de Biotechnologie des Plantes (IBP) - UMR CNRS UPS Bâtiment 630, 91405 Orsay Cedex, France

*To whom correspondence should be addressed. Tel: +33 1 60 87 45 14; Fax: +33 1 60 87 45 49; Email: brunaud{at}evry.inra.fr The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors.

Received July 12, 2007. Revised September 7, 2007. Accepted September 11, 2007.

CATdb is a free resource available at http://urgv.evry.inra.fr/CATdb that provides public access to a large collection of transcriptome data for Arabidopsis thaliana produced by a single Complete Arabidopsis Transcriptome Micro Array (CATMA) platform. CATMA probes consist of gene-specific sequence tags (GSTs) of 150–500 bp. The v2 version of CATMA contains 24 576 GST probes representing most of the predicted A. thaliana genes, and 615 probes tiling the chloroplastic and mitochondrial genomes. Data in CATdb are entirely processed with the same standardized protocol, from microarray printing to data analyses. CATdb contains the results of 53 projects including 1724 hybridized samples distributed between 13 different organs, 49 different developmental conditions, 45 mutants and 63 environmental conditions. All the data contained in CATdb can be downloaded from the web site and subsets of data can be sorted out and displayed either by keywords, by experiments, genes or lists of genes up to 100. CATdb gives an easy access to the complete description of experiments with a picture of the experiment design.


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