A-AFFY-105 - Affymetrix Custom Array - UNIBAS A. gossypii sySYNG001a

Ayshba gossypii
The Affymetrix oligonuceotide arrays used in this study were custom made (GeneChip? CustomExpress? Array Program, Affymetrix, Santa Clara, USA).

The dimension of the chip is 640 x 640 features with 4696 A. gossypii and 20552 C. heterostrophus probe sets. Each A. gossypii probe set consists of 16 antisense probes, each 25 nucleotides long, matching a region within 600 bases from the 3? end of the open reading frame.

The Chip design includes only perfect match (PM) probes with no related mismatch (MM) probes (the PM-MM design is found in some yeast chips). Physical genomic positions of probes are viewed in the Ashbya genome database AGD 3 (Gattiker et al., 2007;
) The 4696 A. gossypii probe sets represent 4452 genes of which 130 do not have a homolog in baker?s yeast (NOHBYs). These are thought to be potential Ashbya-specific genes when compared with S. cerevisiae. When compared with other fungi 40 NOHBYs are Ashbya-specific. 190 of the 4696 probe sets are intergenic or sense probe sets. Affymetrix uses for each probe set an identifier of the pattern ?Ag00XXXX_at?.

Probe sets that have to be used with caution because they are unspecific follow the pattern ?Ag00XXX_*_at?. 31 genes, some of which have particularly long open reading frames (e.g. SPA2, DYN1), are represented by more than one probe set. The 5? to 3? ratios of intensity values of these genes are assessed to check the quality of the ds cDNA and cRNA synthesis steps and RNA integrity (additional information: R. Rischatsch, PhD thesis, 2007;
All experiments done using A-AFFY-105: (E-MEXP-1945, E-MEXP-1954, E-MEXP-1955)
Array DesignA-AFFY-105.adf.txt