High-density rhesus macaque oligonucleotide microarray design using early-stage rhesus genome sequence information and human genome annotations

摘要: Until recently, few genomic reagents specific for non-human primate research have been available. To address this need, we constructed a macaque-specific high-density oligonucleotide microarray by using highly fragmented low-pass sequence contigs from the rhesus genome project together with detailed and exon structure of human genome. Using method, designed probes to over 17,000 distinct rhesus/human gene orthologs increased four-fold number available genes relative our first-generation expressed tag (EST)-derived array. We database containing 248,000 sequences 23,000 RefSeq compared each its best matching in January 2005 version list 486,000 DNA contigs. Best were then concatenated proper order orientation produce "virtual transcriptome." Microarray designed, one per gene, region closest 3' untranslated (UTR) virtual transcript. Each probe was composite transcript test cross-hybridization potential yielding final set representing 18,296 orthologs, including variants, genes. hybridized mRNA brain spleen both EST- genome-derived microarrays. Besides greater coverage, array also showed mean signal intensities present on arrays. Genome-derived 99.4% identity when 4,767 GenBank site (STS) indicating that early stage versions complex genomes are sufficient quality yield valuable functional information combined finished closely related species. The different represented microarrays unfinished can be greatly known annotations species data Signal intensity arrays correlated distance UTR, often missing ESTs yet early-stage projects.