title: NimbleGen Second Generation Apple 26K Array
status: Public on Nov 04 2013
contact.city: University Park
contact.first: Timothy
contact.last: McNellis
contact.state: PA
contact.address: 318 Buckhout Lab
contact.department: Plant Pathology and Environmental Microbiology
contact.country: USA
contact.institute: The Pennsylvania State University
organism: Malus domestica
description: This set includes 60-mer oligonucleotides that are a subset of those in our previous platform, GPL3715.  This second-generation array was a 12-plex array containing 135,000 probes perplex, representing 26,017 transcripts.  This second-generation array represents the transcripts with the best-performing probe sets from the first-generation array and includes the transcripts that showed differential expression between any two scion/rootstock combinations.  Transcripts that had high variability among their probes were left off of the second-generation array. The five best performing probes of the original six probes per transcript were used in the second-generation array to increase the number of different transcripts that could be queried by the second-generation .DNA microarray
manufacture_protocol: NimbleGen proprietary software used to identify 4 or 5 perfectly matched 60-mer oligonucleotides for each apple gene.