title: MJArray Fly
status: Public on Nov 01 2004
contact.city: Karlsruhe
contact.first: Michael
contact.middle: J.
contact.last: Pankratz
contact.email: michael.pankratz@itg.fzk.de
contact.address: P.O. Box 3640
contact.department: Institute of Genetics
contact.country: Germany
contact.web_link: http://www.fzk.de/microarray
contact.institute: Forschungszentrum Karlsruhe
contact.phone: ++49 +7247 82 6087
organism: Drosophila melanogaster
description: The array was assembled using amplicons that were obtained using the Incyte primer set. The set is identical to the one used to produce platform GPL20, primer sequences can be viewed in that platform. We included a reference to the ID of GPL20. The amplicons represent 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.
  
  The regions amplified to build the array ranged in size from 150 to 600 bp with an average size of 410 bp. PCR fragments were amplified and each amplicon was quality control tested for DNA concentration, purity, and fragment size. A total of 11,796 reactions led to a single product of correct size and sufficient amount (marked as ok in column GENE_NAME). The 675 reactions that produced multiple products were run on a gel again and the band of the correct size was excised cloned into pCR TOPO 2.1 (Invitrogen). The 2034 reactions where no band was visible was also subjected to a 'blind' clone-attempt. Those 2709 cloning-reactions led to 2033 positive clones, that were included on the array and marked as 'clone!' in column GENE_NAME. Non sequence-verified clones were not included in the current study. A mixture of all these 2033 clones was used to make a titration dilution as a hybridisation control (Incyte Amplification Titration Standard, IATS) that is included in each of the 48 blocks of our array.
  Arrays were spotted with a Omnigrid 100 (GeneMachines) with 24 SMP3 pins (Telechem). By having two identical subarrays next to each other on each slide, we obtain 48 blocks with 26 rows and 26 columns each. Spot to spot spacing is 150 micron, average spot diameter is 100 micron.