title: CCMB Drosophila Array II
status: Public on May 15 2005
contact.city: Hyderabad
contact.first: L S
contact.last: Shashidhara
contact.email: shashi@ccmb.res.in
contact.state: AP
contact.address: Uppal Road
contact.country: India
contact.web_link: http://www.ccmb.res.in/staff/shashi/droso.html
contact.institute: Centre for Cellular and Molecular Biology
contact.phone: 91-40-27192783
organism: Drosophila melanogaster
description: Primers developed by Incyte Genomics were used to PCR amplify one exon or exon fragment from every predicted gene in the fly genome, using genomic DNA from Cantos-S flies as template. The size, quality and quantity of PCR products were tested by electrophoresis; before and after purification. The array was assembled using amplicons representing approximately 4018 genes predicted in version 1.0 of the Drosophila genome from sequences released by the Berkeley Drosophila Genome Project and Celera Genomics in March 2000. In addition to 4018 genes, Drosophila DNA samples also included several negative controls, particularly intergenic regions.
  
  
  Purified PCR products were concentrated on a speed-vac and resuspended in the printing buffer (0.04 M tris pH 6.5 ,0.1M KCl, 50% DMSO). Average concentration of the DNA used for sporting was ~400 picomoles in 20 ml volume. DNA was spotted in duplicates using the Gen III spotter from Molecular Dynamics on the Type V glass slides provided by Amersham Biosciences, USA. Samples were spotted at a density of 9216 spots per array. All the samples were spotted in duplicates, thus each array carried only 4608 independent samples. In addition to Drosophila DNA samples, each array consisted of as many as 384 spots for positive control, negative control, dynamic range control and ratio control (Amersham Lucidea ScoreCard). These were obtained from Amersham Biosciences. Except for these control spots, contents of CCMB Drosophila Array I and II are the same as in GPL20, although they they do not include all the elements of GPL20.
  
  
  Spotting efficiency was evaluated by Cyber green (Sigma, USA) staining. Dyed or hybridized slides were scanned using Molecular Dynamics GenIII Scanner.