title: CATMA version 2 TIGR 8.0
status: Public on Feb 25 2009
contact.city: Amsterdam
contact.first: Mark
contact.middle: de
contact.last: Jong
contact.address: Kruislaan 318
contact.country: Netherlands
contact.institute: University of Amsterdam
organism: Arabidopsis thaliana
description: CATMA (Complete Arabidopsis Transcriptome MicroArray) is a spotted microarray of Arabidopsis thaliana gene specific tags (GSTs).
manufacture_protocol: Production of the Complete Arabidopsis Transcriptome MicroArray (CATMA)
  
  CATMA (Complete Arabidopsis Transcriptome MicroArray) is a spotted microarray of Arabidopsis thaliana gene specific tags (GSTs). Production took place in a cooperative effort of 12 European research groups [1]. Each group produced part of the 21120 Gene Specific Tags (GSTs), while spotting took place at each individual laboratory. Using a high-resolution spotter enabeled our group to produce all CATMA GSTs on one slide.
  
  GST and primer design
  
  CATMA consists of 21120 GSTs. In order to design these GSTs, a proprietary gene annotation of the Arabidopsis nuclear genome was made with EuGene software [2]. For each annotated gene, a specific region in the first exon was selected and for that region a specific primer pair was designed. Each primer carries a gene-specific 3-prime domain and a 5-prime extension which allowed re-amplification using a small set of extension primers. GST selection and primer design were performed with SPADS software [3].
  
  Amplification
  
  Where possible GSTs were amplified from a collection of IGF[4] and TAMU[5] BAC DNAs. Genomic Col-0 DNA was used if this proved to be impossible. The PCR products were examined by agarose gel electrophoresis, and were only accepted if a single clear band of the correct size was observed. Moreover the sequences of a random selection of BAC-amplified GSTs and in addition all GSTs amplified from genomic DNA were determined. Of 1400 GSTs checked, no incorrect sequences were found. All GSTs were purified, quantified and normalised to 200 ng / µl before spotting.
  
  Spotting
  
  The GSTs are spotted on GAPSII glass slides (Corning) with 48 pins (type 10K) using a MicroGrid II TAS spotter (BioRobotics). A spot size of less than 100 micrometer, and a spot distance of 100 micrometer allows for a total number of 30.000 spots on each slide. Spotting quality is ensured by sampled analysis of deposited buffer salt chrystals, ethidium bromide staining and test hybridisations.
  
  Batch-wise processing
  
  To track the quality of each slide, bar codes are used to administer the spotting runs, and the manufacturers production batch. This provides the ability to quickly recognise series of slides with spotting defects and even the ability to recall certain groups of slides.
  
  Conclusion
  
  The CATMA microarray consists of GSTs that are based on modern gene annotation software which provide a minimal level of sequence overlap. Production of the slides takes place under stringent conditions ensuring high quality and reproducability over a wide range of experiments.
  
  Remarks
  
  1. The general homepage with the contributing groups can be found at www.catma.org
  2. Schiex, T, Moisan, A, and Rouzé, P (2001), EUGENE: An Eukaryotic Gene Finder That Combines Several Sources of Evidence, Lecture Notes in Computer Sciences 2066: 111-125
  3. SPADS is available on the internet: genoplante-info.infobiogen.fr/spads/
  4. Mozo T, Fischer S, Shizuya H, Altmann T (1998) Construction and characterization of the IGF Arabidopsis BAC library, Molecular and General Genetics 258(5):562-70
  5. TAMU BAC DNA: hbz.tamu.edu/bac.html