During recent years, Arabidopsis thaliana (Thale cress) has become the most important model species for plant physiology and genetics. In 2000, the Arabidopsis genome was the first plant genome to be sequenced making it the third eukaryote genome to be completed (1). Therefore, it was not surprising that Arabidopsis became the main model plant for plant functional genomics as well. Several microarrays were developed to probe the Arabidopsis transcriptome, and the Affymetrix AG and ATH1 GeneChip® arrays are currently the most widely used.

Development of the first Arabidopsis microarrays was driven by community needs. In the US, NSF supported the development of a spotted microarray with around 11000 cDNAs (2). In parallel, the Novartis Agriculture Discovery Institute, Inc. (NADII) and Affymetrix together developed the first Arabidopsis GeneChip® array. This AG GeneChip® array contains around 8300 probe sets (3) and in 2000 Affymetrix made this microarray publicly available. Again supported by the NSF, the Institute for Genomic Research (TIGR) and Affymetrix developed a second Arabidopsis GeneChip® array. Because this ATH1 GeneChip® array contains more than 22 000 probe sets, that is it probes nearly every Arabidopsis gene, it is commonly referred to as a 'full genome microarray' (4). Importantly, a systematic comparison of AG and ATH1 microarrays showed that results were consistent between both microarray generations (5).

In the meantime additional Arabidopsis microarrays were developed by both academic consortia and commercial service providers. The EU-supported CAGE consortium constructed the CATMA microarray, which contains nearly 20000 cDNAs ( The Agilent Arabidopsis 3 Oligo Microarray Kit uses 60-nucleotide oligomers to probe 40000 Arabidopsis transcripts (including non-coding transcripts). Qiagen Operon offers a set of nearly 30 000 70-nucleotide oligomers that has been used to study flower development in Arabidopsis (6). In addition to Arabidopsis, microarrays for other plant species are entering the market as well. They include barley, grape and soybean Affymetrix GeneChip® arrays, oligonucleotide sets for grape, Medicago and peach from Operon and rice oligonucleotide microarrays from Agilent.

Here, I will describe the typical work-flow of an RNA profiling experiment in Arabidopsis using Affymetrix GeneChip® arrays.

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