title: Univ of Jyvaskyla Drosophila montana microarray 197
status: Public on Mar 04 2010
contact.city: Jyvaskyla
contact.first: Maaria
contact.last: Kankare
contact.email: maaria.kankare@jyu.fi
contact.address: Survontie 9
contact.country: Finland
contact.institute: University of Jyvaskyla
organism: Drosophila montana
description: The primers for the candidate genes of D. montana were designed for one to three 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 mentioned above. Next, an online program e-Array 5.3 (Agilent) was used to design one to four 60 bp oligonucleotide probes per gene 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-colour system.
manufacture_protocol: The species-specific candidate gene microarray constructed for D. montana included 101 genes known to affect circadian clock (25 genes), phototransduction (26 genes), diapause (7 genes) and courtship behaviour (13 genes) as well as responses to cold (2 genes) and heat (28 genes) in D. melanogaster. The genes were selected from the D. melanogaster genome using FlyBase gene ontology searches on biological response (http://flybase.org/). The most conserved regions of the candidate genes were indentified by aligning the exon regions of the D. melanogaster gene to their orthologs in D. virilis with Blat search in UCSC Genome Bioinformatics database (http://genome.ucsc.edu).