Comparison of gene expression profile of bovine muscle samples

A bovine oligo microarray platform (GPL7053) was used to profile gene expression from twenty-five (25) bovine biceps brachii samples randomly collected at the slaughterhouse. Four (4) of these animals were suspected for corticosteroids treatment at tymus histological analyses. Eighteen (18) negative controls animals were also included. Analysis with PAM (Prediction Analysis of Microarray) identified ten (10) genes as potential biomarkers that best discriminated control animals from the animals suspected for corticosteroids treatment. In this study, we analyzed forty-three (43) bovine muscle samples, twenty-five (25) unknown samples and eighteen (18) negative controls. Gene expression profiling was performed using the Agilent-015354 Bos taurus Oligo Microarray platform (GPL7053) 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.