MICROARRAYS
Agilent Technologies
Macaque DNA microarrays are an important resource for investigators interested in gene expression profiling ofmacaque cells and tissues. Using sequence data from the rhesus macaque genome project, we have developed a second-generation macaque oligonucleotide microarray. This array is available through Agilent Technologies and contains 60-mer oligonucleotide sequences corresponding to over 17,000 distinct rhesus macaque transcripts, approximately 1,000 human genes, and 96 viral genes (representing 27 different viruses).
To design probes for this array, we constructed a database containing 248,000 exon sequences from 23,000 human RefSeq genes and compared each human exon with its best matching sequence in the January 2005 version of the rhesus genome project list of 486,000 DNA contigs. Best matching rhesus exon sequences for each of the 23,000 human genes were then concatenated in the proper order and orientation to produce a rhesus "virtual transcriptome." Microarray probes were then designed to the region closest to the 3' untranslated region of each rhesus virtual transcript. A complete description of the design strategy is available in Wallace et al., BMC Genomics 8:28, 2007.
Our cDNA library construction and EST sequencing projects also served to generate the nucleotide sequence data needed to construct a first-generation microarray containing approximately 4,000 distinct rhesus macaque oligonucleotide sequences. An analysis of the sequence data underlying this original array can be found in Magness et al, Genome Biol. 6:R60, 2005.
Affymetrix
Affymetrix has also developed a GeneChip rhesus macaque genome array based on sequence data from the October 2004 version of the rhesus genome project along with GenBank rhesus EST, STS and mRNA sequences up to March 30, 2005.