title: University of of Jyvaskyla FIN D. montana and D. virilis microarray 219
status: Public on Oct 01 2011
contact.city: Jyväskylä
contact.first: Laura
contact.last: Vesala
contact.email: laura.vesala@jyu.fi
contact.address: Survontie 9
contact.department: Department of Biological and Environmental Science
contact.country: Finland
contact.institute: University of Jyväskylä
organism: Drosophila virilis
  Drosophila montana
description: The array contains multiple probes per a particular gene, designed separately for the two study species, using species-specific sequences (either D.montana or D. virilis).
manufacture_protocol: Since there is no genome sequence available for D. montana (and only partial annotations for D. virilis genome), we selected genes on the array from the D. melanogaster genome using FlyBase gene ontology searches on biological response of interest (http://flybase.org/). The most conserved regions of the candidate genes were then identified by aligning the exon regions of the D. melanogaster gene sequence to their orthologs in D. virilis with Blat search in UCSC Genome Bioinformatics database (http://genome.ucsc.edu). The primers for the candidate genes of D. montana and D. virilis were designed for one to four unique 200-500 bp regions with Primer3 program (http://www-genome.wi.mit.edu/genome software/other/ primer3.html) or manually, using information on the gene alignments. Next, an online program e-Array 5.3 (Agilent) was used to design one to four 60 bp oligonucleotide probes per gene (based on species-specific sequences) using exon regions. Finally, the probes were synthesized in situ with liquid chemistry and arrayed on an “Agilent 60-mer Multi-Pack Gene Expression Microarray” platform with one-color system.