Plant Physiology 137:588-601 (2005)
© 2005 American Society of Plant Biologists
GENOME ANALYSIS
Benchmarking the CATMA Microarray. A Novel Tool forArabidopsis Transcriptome Analysis1,[w]
Joke Allemeersch,
Steffen Durinck,
Rudy Vanderhaeghen,
Philippe Alard,
Ruth Maes,
Kurt Seeuws,
Tom Bogaert,
Kathleen Coddens,
Kirsten Deschouwer,
Paul Van Hummelen,
Marnik Vuylsteke,
Yves Moreau,
Jeroen Kwekkeboom,
André H.M. Wijfjes,
Sean May,
Jim Beynon,
Pierre Hilson2 and
Martin T.R. Kuiper2,*
Department of Electrical Engineering (ESAT), Faculty of Engineering, Katholieke Universiteit Leuven, B–3001 Heverlee, Belgium (J.A., S.D., Y.M.); Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology (VIB), Ghent University, B–9052 Gent, Belgium (R.V., P.A., M.V., P.H., M.T.R.K.); VIB MicroArray Facility, Campus Gasthuisberg, B–3000 Leuven, Belgium (R.M., K.S., T.B., K.C., K.D., P.V.H.); ServiceXS, 2333 AL Leiden, The Netherlands (J.K., A.H.M.W.); Nottingham Arabidopsis Stock Centre, Division of Plant Sciences, University of Nottingham, Sutton Bonington LE12 5RD, United Kingdom (S.M.); and Warwick HRI, University of Warwick, Warwick CV35 9EF, United Kingdom (J.B.)
Transcript profiling is crucial to study biological systems, and various platforms have been implemented to survey mRNAs at the genome scale. We have assessed the performance of the CATMA microarray designed for Arabidopsis (Arabidopsis thaliana) transcriptome analysis and compared it with the Agilent and Affymetrix commercial platforms. The CATMA array consists of gene-specific sequence tags of 150 to 500 bp, the Agilent (Arabidopsis 2) array of 60mer oligonucleotides, and the Affymetrix gene chip (ATH1) of 25mer oligonucleotide sets. We have matched each probe repertoire with the Arabidopsis genome annotation (The Institute for Genomic Research release 5.0) and determined the correspondence between them. Array performance was analyzed by hybridization with labeled targets derived from eight RNA samples made of shoot total RNA spiked with a calibrated series of 14 control transcripts. CATMA arrays showed the largest dynamic range extending over three to four logs. Agilent and Affymetrix arrays displayed a narrower range, presumably because signal saturation occurred for transcripts at concentrations beyond 1,000 copies per cell. Sensitivity was comparable for all three platforms. For Affymetrix GeneChip data, the RMA software package outperformed Microarray Suite 5.0 for all investigated criteria, confirming that the information provided by the mismatch oligonucleotides has no added value. In addition, taking advantage of replicates in our dataset, we conducted a robust statistical analysis of the platform propensity to yield false positive and false negative differentially expressed genes, and all gave satisfactory results. The results establish the CATMA array as a mature alternative to the Affymetrix and Agilent platforms.
1 This work was supported in part by the 5th European Framework Programme (Compendium of Arabidopsis Gene Expression; grant no. QLK3–CT–2002–02035).
2 These authors contributed equally to the paper.
[w] The online version of this article contains Web-only data.
www.plantphysiol.org/cgi/doi/10.1104/pp.104.051300.
* Corresponding author; e-mail martin.kuiper{at}psb.ugent.be; fax 32–9–3313809.
Received August 6, 2004;
returned for revision November 9, 2004;
accepted November 18, 2004.
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