title: Affymetrix/NimbleGen Candida glabrata array [CaGl04a530005N]
status: Public on Jan 01 2011
contact.city: Memphis
contact.first: Katherine
contact.middle: S
contact.last: Barker
contact.email: ksbarker@uthsc.edu
contact.state: TN
contact.address: 881 Madison Avenue, Room 305
contact.department: Clinical Pharmacy
contact.country: USA
contact.institute: University of Tennessee Health Science Center
organism: Nakaseomyces glabratus
manufacture_protocol: The nucleotide sequences corresponding to 5272 C. glabrata ORFs were downloaded from the Génolevures Consortium (http://cbi.labri.fr/Genolevures/about.php, Build 2). Following the Affymetrix Design Guide, two separate probe sets for each ORF were designed, each consisting of 13 perfect match and 13 mismatch overlapping 25 base oligonucleotides targeted to the 3? 600 bp region. For ORFs < 600 bp the sequence was divided in two equal segments for subsequent design procedures. For quality control and normalization purposes, we designed two to three additional probe sets spanning the C. glabrata 18 s rRNA, TDH1 and ACT1 genes in addition to standard Affymetrix controls (BioB, C, D, cre, DAP, PHE, LYS, THR). The probe selection was performed by the Chip Design group at Affymetrix, using their proprietary algorithm to calculate probe set scores, which includes a probe quality metric, cross-hybridization penalty, and gap penalty. The probe sets were then examined for cross-hybridization against all other sequences in the C. glabrata genome as well as a number of constitutively expressed genes and rRNA from other common organisms. Duplicate probesets are made to distinct regions of the ORF, thereby allowing two independent measurements of the mRNA level for that particular gene. C. glabrata custom Affymetrix NimbleExpress Arrays were manufactured by NimbleGen Systems per our specification.