Comparison of gene expression profile of bronchoalveolar lavage fluid (BAL) from RAO- and IAD- affected horses with respect to control animals

An equine immuno-specific oligo microarray platform was designed to evidence differences in gene expression profiles in BAL fluid samples from eight (8) RAO-affected horses, ten (10) IAD-affected horses and seven (7) control animals. An unpaired t test was performed using the software Significant Analysis of Microarrays (SAM). 1763 and 379 genes were found differentially expressed between RAO and IAD horses respectively vs. controls. In this study, we analyzed twenty-five (25) equine BAL fluid samples: seven (7) from control animals, eight (8) from recurrent airway obstruction (RAO)-affected horses and ten (10) from inflammatory airway disease (IAD)-affected horses. Gene expression profiling was performed using an equine immuno-specific oligo microarray platform based on single-colour detection (Cyanine-3 only). Microarrays were scanned with Agilent scanner G2565BA (barcode on the left, DNA on the back surface, scanned through the glass) at a resolution of 5 microns; all slides were scanned twice at two different sensitivity settings (XDRHi 100% and XDRLo 10%); the scanner software created a unique ID for each pair of XDR scans and saved it to both scan image files. Feature Extraction (FE) 9.5 used XDR ID to link the pairs of scans together automatically when extracting data. The signal left after all the FE processing steps have been completed, is ProcessedSignal that contains the Multiplicatively Detrended, Background-Subtracted Signal.