title: Drosophila Incyte arrays, Klebes/Kornberg v1
status: Public on Jul 08 2005
contact.city: Berlin
contact.first: Ansgar
contact.last: Klebes
contact.email: ansgar.klebes@web.de
contact.address: Chausseestr. 117
contact.department: Biology
contact.country: Germany
contact.institute: Humboldt University Berlin
contact.phone: +49-30-20938174
organism: Drosophila melanogaster
description: The array was assembled using amplicons representing approximately 93% of the 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. The amplicons represent approximately 75% of the genes predicted in the January 2003 release 3.1 Drosophila genome annotation update.
  Incyte in-house algorithms were used to develop gene-specific primers averaging 20 nucleotides in length that were used to PCR amplify one exon or exon fragment from every predicted gene in the fly genome. The regions amplified to build the array ranged in size from 150 to 600 bp with an average size of 410 bp.
  
  Additionally, non-Drosophila sequences (Adenovirus, GFP) were spotted for spiking controls, background control, and orientation purposes.
  
  Hybridized slides were read with a GenePix 4000A scanner (Axon Instruments, Foster City, CA).
manufacture_protocol: The arrays were produced essentially as Brian Oliver's 'Incyte Drosophila LifeArray v1.0', GEO platform GPL20.
  
  These arrays were described in Xu et al., Human Molecular Genetics, 2003, Vol. 12, No. 2 169-175; and Klebes et al., Development, 2005, in press.
  
  In brief: The Easy-to-Spot Drosophila ORF PCR Primer Set (Incyte Genomics Inc.) with 14 151 primer pairs to unique open reading frames and additional control sequences was used for PCR amplification. The amplicons represent non-intronic sequences. All PCR products were analyzed on agarose gels and a success rate of >94% was estimated. Reactions were arrayed into 384-well plates and printed on poly-L-lysine-coated glass slides using a linear servo arrayer and ArrayMaker version 2 control software.