title: MdoFruit_UCDavis_ADand_052606_4302_12k
status: Public on Aug 17 2010
contact.city: Davis
contact.first: Abhaya
contact.middle: M
contact.last: Dandekar
contact.email: amdandekar@ucdavis.edu
contact.state: CA
contact.address: One Shields Ave
contact.department: Plant Sciences
contact.country: USA
contact.institute: University of California, Davis
contact.phone: 530 752 7784
organism: Malus domestica
description: In a few instances, targets of oligo probes lack a GenBank accession. The sequences of these and all probes on the array are included in the platform table.
manufacture_protocol: Oligonucleotide probes for the entire array were designed in one step using an algorithm provided by CombiMatrix. Probes 35-40 nt in length with predicted Tms within a 5ºC window were randomly distributed across the surface of the array in a layout file. This was used to direct synthesis of oligonucleotides at each site on the array. A total of 12,395 probes were synthesized, of which 474 were control probes and 11,921 probes represented apple genes.
  Using CustomArray 12k (oligonucleotide), probes were synthesized directly on the chip surface, composed of a proprietary porous reaction layer. 12k arrays consist of 12,000 user definable oligonucleotide features, 35-40 nt optimum. Under each probe, a semiconductor electrode used electrochemical detritylation to control sequence synthesis at that spot without a physical mask as in lithographic synthesis. The process yields a 44 micron feature with 1.5 picomole sensitivity. The arrays were designed for one-color biotinilated hybridization experiments.