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This model considers hybridization only on one spot on the microarray.
We simulate hybridization reactions for one spot on the microarray, which is considered to be a sample chamber with two compartments; a spot phase and a solution phase.
We determined the median ratio of each spot on the microarray from the four independent hybridizations, and also calculated a p-value for significant ratios using a previously described error model [25], [26].
Thus, the glycan-related gene expression profiles are expressed as the ratio of the gene expression signal at each spot on the microarray relative to the reference RNA signal.
The analysis compared the expression levels of every single spot on the microarray relative to a reference sample, and then compared the relative expression levels between stressed and control birds, or between birds whose parents had received stress or control treatment.
Each spot on the microarray is composed of the proteins secreted by a single cell.
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Of the 3,528 CDSs spotted on the microarray slides, 275 were considered absent from at least one of the L. interrogans strains tested.
Gene Name & Gene Symbol: gene identity of best BLAST match homologue to cDNA or plasmid; GenBank ID: Accession number of equine cDNA spotted on the microarray; Fold Change (N/A): Relative Neonate/Adult fold change; p-value: one-sample t-test p-value for probe across the four biological replicates in the total sample set.
Of the 3,581 genes spotted on the microarray, 98 (2.7%) were found to be absent in at least one of the B. pertussis strains tested.
A total of 244 oligonucleotides (26 to 37 nucleotide length and with similar melting temperatures) were spotted on the microarray, including genes conferring resistance to clinically important antibiotic classes like β-lactams, macrolides, aminoglycosides, glycopeptides and tetracyclines.
Improved purification, solubilization, and quantification of proteins spotted on the microarray would likely make this a more reliable assay.
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