CATMA: A Complete Arabidopsis transcriptome Microarray

The CATMA database is publicly and freely available. Access it here

The aim of the Complete Arabidopsis Transcriptome MicroArray (CATMA) project was the design and production of high quality Gene-specific Sequence Tags (GSTs) covering most Arabidopsis genes. The GST repertoire is used by numerous groups for the production of DNA arrays for transcript profiling experiments.

CATMA microarrays constitute the foundation of the CAGE project aiming at the construction of a gene expression reference database for Arabidopsis. The CATMA GSTs are also the basic materials in the AGRIKOLA project focusing on the large-scale systematic RNAi silencing of Arabidopsis genes.

CATMA is a consortium of research groups from eight European countries. All CATMA members are public laboratories, some with ties to private research institutions. In the years 2001 to 2003, they contributed to the purchase of the reagents and to the work necessary for the production of the version 1 (v1) and v2 GST repertoires.

A synchronization of the repertoire in 2005 with the at that time latest Arabidopsis genome annotations (TIGR5 and Eugène040917)lead -with financial support of the French, German, Swedish, Swiss, UK and Belgian members- to repertoire v3 containing 30,343 GSTs. A last design effort was undertaken in 2006 by the Swiss consortium member, in which an extra 543 GSTs could be designed by using less stringent design criteria, thus forming repertoire v4. Probes were now also allowed to simultaneously tag multiple members of gene families, leading to 990 GFTs (Gene Family Tags). The description of these GFTs can be found on the CATMA Gene Family Tag website.

CATMA co-ordinators 

Coordinator
Pierre Hilson
France
Jean-Pierre Renou
Germany
Wilfried Nietfeld
Netherlands
Peter Weisbeek
Spain
Javier Paz-Ares
Sweden
Rishikesh Bhalerao
Switzerland
Philippe Reymond
United Kingdom
Jim Beynon
Bioinformatics
Martin Kuiper

Platforms providing a service based on CATMA materials

http://arabidopsis.info/
The Nottingham Arabidopsis Stock Centre (NASC) distributes GST PCR amplicons and spotted arrays. NASC also distributes E. coli strains carrying GST entry and hairpin RNA expression Gateway clones from the AGRIKOLA project.
http://bccm.belspo.be/db/lmbp_gst_clones/
The Belgian resource center BCCM/LMBP provides purified and sequence-validated GST entry and hairpin RNA expression Gateway clones from the AGRIKOLA project.
http://www.psb.ugent.be/reva
The Department of Plant Systems Biology (VIB-UGent) accepts on line requests for AGRIKOLA clone sequence validation. When available, such clones are distributed by BCCM/LMBP.
http://www.partnerchip.fr/
The PartnerChip service facility, in collaboration with the Unité de Recherche en Génomique Végétale (URGV) , provides CATMA microarray hybridization and analysis services.
http://urgv.evry.inra.fr/CATdb
CATdb provides all transcriptome data generated by the URGV CATMA platform. As of February 2007, CATdb contains results from 47 projects (1372 hybridizations). These figures are expected to double in the coming year.

Links

CATMA received the support of the following organisations:

VIB VIB MAF garnet BBSRC Genoplante NASC MPG GABI UPSC JIC Lausanne Utrecht Plant Systems Biology