Affymetrix appears to offer the most extensive list of model organism microarrays. The list ranges from Bacillus subtilis to rat and rice. They introduced eight new designs in 2004 and plan on launching seven more during 2005.
The model organism arrays offered this year include sugarcane, canine, medicago, rhesus macaque, citrus, tomato, and poplar. Affymetrix has plans to continue to expand the list, adds McLean.
The Affymetrix GeneChip microarrays combine semiconductor fabrication techniques with biochemistry to create a photolithographic manufacturing process capable of producing microarrays with millions of probes on a single glass chip. GeneChip technology continues to have tremendous room for growth, allowing for higher densities and more content on the same sized arrays, says McLean.
Affymetrix offers C. elegans and Drosophila whole genomic microarrays. The C. elegans array contains 25mer oligonucleotide probes synthesized in situ and designed to measure gene expression in over 22,500 transcripts. The array was designed using the December 2000 genome sequence, predicted transcripts, and EST sequences from the Sanger Center.
The Drosophila genome array was developed from sequences accessible through FlyBase. The 25mer oligo probes represent a total number of 13,500 transcripts.
Both C. elegans and Drosophila microarrays can be used to study genes involved in development, analyze the global effect of mutations, and build quantitative gene expression databases. Since C. elegans and Drosophila are model systems for crop safety and pesticides research, these arrays can be used to study gene expression changes upon exposure to pesticides and crop treatments.
Affymetrixs GeneChip Plasmodium/ Anopheles is the first microarray to provide comprehensive coverage of two organisms on a single array, interrogating over 20,000 transcripts from the malarial parasite Plasmodium falciparum and the mosquito, Anopheles gambiae.
The inclusion of both organisms on a single array allows scientists to better understand the molecular dynamics involved in the host-parasite relationship as well as the mechanism of action and biology behind malaria.
Whole genome microarrays can make excellent starting points for discovering genes that are involved in specific pathways. Scientists can use the whole organism microarrays to perform genome-wide screens for target validation, toxicity screening, or signaling pathway research and then follow up with other assays such as Taqman to validate the microarray results, says Burrill.
Taqman assay is a quantitative PCR assay that can be used for DNA copy number measurements, single nucleotide polymorphism genotyping, or verification of microarrays results.
Once you get a gene list from genomic screens and find their biological functions, it is possible to draw up a list of interesting genes that are related or act in the same or related pathways. This smaller subset of genes can then be studied more intensively using smaller custom microarrays.