The microarray design included 4,320 spots arranged in 48 blocks of 90.
Microarray design included genes from functional categories which were expected to be affected by stress (Table 2).
In addition to standard Affymetrix controls, positive controls in the microarray design included probes for constitutively expressed Sorghum bicolor genes (actin, ubiquitin and eIF4a1).
The microarray design includes 40,924 oligonucleotide probes for analysis of gene expression in lichen samples.
The microarray design, including oligo sequences and SNP information is available by request from the authors.
A complete description of this microarray design, including the exact sequence for each spot on the array and the associated data files, is available as part of the GEO platform description for this microarray (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi acc=GPL9464).nih.gov/geo/query/acc.cgi acc=GPL9464
As mentioned earlier, CG dinucleotides are very mutable and polymorphic, which is a problem for microarray designs that include a substantial component of CGs that represent known common SNPs [ 118, 119].
The most widely used microarray experiment design includes the use of a reference standard.
A new microarray was designed including both coding sequences and intergenic regions to investigate the acetate stress responses of Zymomonas mobilis 8b when using single carbon sources of glucose or xylose, or mixed sugars of both glucose and xylose.
CGH were performed against an Affymetrix custom microarray designed to include 2,661 977%) chromosomal and 17 (85%) plasmid CDSs predicted to occur in L. casei ATCC 334 as well as all predicted CDSs in the draft L. helveticus CNRZ 32 genome (Smeianov et al. 2007).
Hence, the quality of the microarrays design which includes selecting short Oligonucleotide sequences (probes) to be affixed on the surface of the microarray becomes a major issue.
