title: [CAN04a530004N] Candida albicans affymetrix array
status: Public on Aug 17 2007
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: The nucleotide sequences corresponding to 6165 open reading frames (ORFs) for C. albicans were downloaded from the Galar Fungail European Consortium (Assembly 19, http://www.pasteur.fr/Galar_Fungail/CandidaDB/). Following the Affymetrix Design Guide, we set out to design two separate probe sets for each ORF, each consisting of 13 perfect matches and 13 mismatches 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 2-3 additional probe sets spanning the entire sequence of the C.  albicans 18S rRNA (GenBank Accession M60302), genes encoding GAPDH, actin and Mdr1p (Bmr1p) 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 10,736 probesets including 9 controls, 6,123 unique ORFs and duplicate probesets for 4,604 ORFs. The duplicate probesets are made to distinct regions of the ORF, thereby allowing 2 independent measurements of the mRNA level for that particular gene. The C. albicans custom Affymetrix NimbleExpress Arrays (CAN04a530004N) were manufactured by NimbleGen Systems per our specification.