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Platform GPL9293 Query DataSets for GPL9293
Status Public on Mar 04, 2010
Title Univ of Jyvaskyla Drosophila montana microarray 197
Technology type in situ oligonucleotide
Distribution custom-commercial
Organism Drosophila montana
Manufacturer Agilent
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).
Catalog number G2509F
Support glass
Coating unknown
 
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.
 
Contributor(s) Kankare M, Salminen T, Laiho A, Vesala L, Hoikkala A
Submission date Sep 25, 2009
Last update date Mar 04, 2010
Contact name Maaria Kankare
E-mail(s) maaria.kankare@jyu.fi
Organization name University of Jyvaskyla
Street address Survontie 9
City Jyvaskyla
ZIP/Postal code 40014
Country Finland
 
Samples (9) GSM456444, GSM460021, GSM460057, GSM460058, GSM460059, GSM460060 
Series (1)
GSE18475 Gene expression in Drosophila montana

Data table header descriptions
ID
GeneName Name of the gene used in the array
GENE SYMBOL
ProbeName Probe name by Agilent
SEQUENCE 60-mer sequence of the probe
SPOT_ID

Data table
ID GeneName GENE SYMBOL ProbeName SEQUENCE SPOT_ID
875 Adar_1F1R Adar CUST_1_PI358506070 CTGATATACACGTTGATGTTGCCTGCAAAGAAATCCAACCTTACCTCGCTTGAACAACCC Adar_1F1R
15614 Adar_2F2R Adar CUST_1_PI358506159 AATTCATGTTTTCTGTCATAACTATGCCTGCCAGTACTTTTCGCCGAGAGTACGCCTCCT Adar_2F2R
10951 Adh_1_1_i Adh CUST_14_PI373864400 AAAGCATCACTAAGAGTATGGCGATCGCAAACAAGAACATCATCTTTGTCGCTGGACTGG Adh_1_1_i
12392 Adh_1_2_i Adh CUST_4_PI373864400 TTACATTCTATCCCTATGATGTAACTGTGCCGGTGGCAGAAACCACAAAGCTGCTGAAGA Adh_1_2_i
9282 Ankyrin_1_L Ankyrin CUST_11_PI371460617 TCTTATGCTCAATTACGGGTGGACAGAATCGAGCTATTTGGGAGGATGTTACTGGGTCAA Ankyrin_1_L
13454 Ankyrin_1R Ankyrin CUST_1_PI358506163 TAGCGTTAGCTTTACCACAACCGTATCGGCACGCTTTTGGCTAATGGATTGTCGCAATTA Ankyrin_1R
11896 ariadne_1F1R ariadne CUST_8_PI374126204 ATATGGTCTGCAAGAATCAAAATTGCAAGCATGACTTTTGCTGGGTATGCCTCGGCTCCT ariadne_1F1R
11512 ariadne_2F2R ariadne CUST_10_PI374126204 AATATCAGCAGCTGATCACCAATAGTTTTGTTGAATGCAATCAGCTGCTGCGCTGGTGTC ariadne_2F2R
888 Arr1_1F1R Arr1 CUST_1_PI358506167 TTCGCATAGGCGCAGCACCATTAACCTGGGCATACGCAAGGTGCAGTATGCACCCACCAA Arr1_1F1R
27 Arr1_2 Arr1 CUST_11_PI367339995 GGCTAATTGTGATCGGGCTGGCATTGCCGTTGAGGGCGATATCAAGCGCAAGGACACAGA Arr1_2
10759 Arr2_2R Arr2 CUST_5_PI373864398 CCGAGGACGATCGTCAGCACAAGCGCAGCATGGTCAGTCTGGTGATCAAGAAGCTGCAAT Arr2_2R
2336 atonal_1_1L atonal CUST_12_PI373864402 TGGCGAGATTTGCTTATTGCGACGCTTCTTTCCGGTGCCGGCTGTGGATGCGTTGGGATT atonal_1_1L
9852 atonal_1_2L atonal CUST_8_PI373864402 TCGAAATCAAAACTCTGGAAGTCGTCGGAATAGAGCTGGACATTGGAGTTGTTGCTCTGT atonal_1_2L
2774 atonal_1_3L atonal CUST_2_PI373864402 TTGCATGTGCCCACATTAGGTGAGCCCATAATCTCCAAAGCTGGCTGTGGAGCAGGCGCT atonal_1_3L
14324 black_1F1R black CUST_1_PI358506169 TTGTTGGCTTTCCAAACAATGGCCACGGCGATGGCATCTTCTGTCCAGGCGGCTCGATAG black_1F1R
4542 black_2F2R black CUST_1_PI358506171 ATATTCACGTCGGAGGATGCACATTACTCCGTAGAAAAGCTGGCCATGTTTATGGGCTTT black_2F2R
2982 btv_1F1R btv CUST_1_PI374126204 TGCGATGGCAGCATTGATCCCGAGTGGATTGAGGCATTAAACTCGGTACTGGACGATAAC btv_1F1R
11739 btv_2F2R btv CUST_6_PI374126204 ATCATGCTGCAGTGGGAGCAACTGCAGCCGCTGCTGGAGAACCATGCGGTCATATTGCAA btv_2F2R
3281 btv_3F btv CUST_2_PI373864400 AGTATATACTCGGCCTGCTCGACATGAACAACAAATTGCCGGATATACATATAAAGCTGG btv_3F
12340 cac_3_1 cac CUST_4_PI373864398 TAGCAAAGGCTTTGATTGCGATCGCGTAATCCAAAGGAACAGATCTGGGTATAGCATCAG cac_3_1

Total number of rows: 197

Table truncated, full table size 21 Kbytes.




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