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.
Up-regulation of ERG11 is prevalent among azole-resistant clinical isolates of Candida albicans and is only partially explained by gain-of-function mutations in UPC2
"B. subtilis /GEN=lys /DB_XREF=gb:X17013.1 /NOTE=SIF corresponding to nucleotides 387-658 of gb:X17013.1, not 100% identical /DEF=B subtilis lys gene for diaminopimelate decarboxylase (EC 4.1.1.20)."
control
AFFX-LysX-M_at
"B. subtilis /GEN=lys /DB_XREF=gb:X17013.1 /NOTE=SIF corresponding to nucleotides 720-990 of gb:X17013.1, not 100% identical /DEF=B subtilis lys gene for diaminopimelate decarboxylase (EC 4.1.1.20)."
control
AFFX-LysX-3_at
"B. subtilis /GEN=lys /DB_XREF=gb:X17013.1 /NOTE=SIF corresponding to nucleotides 1061-1343 of gb:X17013.1, not 100% identical /DEF=B subtilis lys gene for diaminopimelate decarboxylase (EC 4.1.1.20)."
control
AFFX-PheX-5_at
"B. subtilis /GEN=pheA /DB_XREF=gb:M24537.1 /NOTE=SIF corresponding to nucleotides 2028-2375 of gb:M24537.1, not 100% identical /DEF=Bacillus subtillis sporulation protein (spoOB), GTP-binding protein (obg), phenylalanine biosynthesis associated protein (pheB), and monofunctional prephenate dehydratase (pheA) genes, complete cds."
control
AFFX-PheX-M_at
"B. subtilis /GEN=pheA /DB_XREF=gb:M24537.1 /NOTE=SIF corresponding to nucleotides 2437-2828 of gb:M24537.1 /DEF=Bacillus subtillis sporulation protein (spoOB), GTP-binding protein (obg), phenylalanine biosynthesis associated protein (pheB), and monofunctional prephenate dehydratase (pheA) genes, complete cds."
control
AFFX-PheX-3_at
"B. subtilis /GEN=pheB /DB_XREF=gb:M24537.1 /NOTE=SIF corresponding to nucleotides 2885-3326 of gb:M24537.1, not 100% identical /DEF=Bacillus subtillis sporulation protein (spoOB), GTP-binding protein (obg), phenylalanine biosynthesis associated protein (pheB), and monofunctional prephenate dehydratase (pheA) genes, complete cds."
control
AFFX-ThrX-5_at
"B. subtilis /GEN=thrC /DB_XREF=gb:X04603.1 /NOTE=SIF corresponding to nucleotides 288-932 of gb:X04603.1 /DEF=B. subtilis thrB and thrC genes for homoserine kinase and threonine synthase (EC 2.7.1.39 and EC 4.2.99.2, respectively)."
control
AFFX-ThrX-M_at
"B. subtilis /GEN=thrC, thrB /DB_XREF=gb:X04603.1 /NOTE=SIF corresponding to nucleotides 995-1562 of gb:X04603.1, not 100% identical /DEF=B. subtilis thrB and thrC genes for homoserine kinase and threonine synthase (EC 2.7.1.39 and EC 4.2.99.2, respectively)."
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