title: [CAN07a520619F] Candida albicans 11-mer Affymetrix 10K array version1
status: Public on Nov 05 2008
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: Candida albicans
manufacture_protocol: We developed a new Affymetrix custom expression array (CAN07, 49-5241 array format with 11 micron features) for C. Albicans.  The nucleotide sequences corresponding to 6,165 open reading frames (ORFs) for C. albicans were downloaded from the Galar Fungail European Consortium (Assembly 6, http://www.pasteur.fr/Galar_Fungail/CandidaDB). We planned to design two separate probe sets for each ORF, each consisting of 11 perfect match and 11 mismatch overlapping 25 bp oligonucleotides, to the 3’ 600 bp region. For ORFs less than 600 bp in length the sequence was divided in two equal segments for subsequent design procedures. For quality control and normalization purposes, we made additional control probesets corresponding to GAPDH (1 probeset), actin (1 probeset) and the 5’ and middle region of Mdr1p (Bmr1p) transcript in addition to the standard Affymetrix controls (BioB, C, D, cre, DAP, PHE, LYS, THR). The probe selection was performed by the Chip Design group at Affymetrix, Inc. 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. albicans genome as well as a number of constitutively expressed genes and rRNA from other common organisms. Consequently, for some target regions we were not able to design high quality probe sets. In the end, the GeneChip contained 10,014 probesets, corresponding to 5,806 unique ORFs. Two probes were represented for 4,208 ORFs, allowing 2 independent measurements of the mRNA level for that particular gene.