Comparison of gene expression profile of biceps brachii muscle samples from prednisolone-treated and control cows

A bovine oligo microarray platform (GPL7053) was used to evidence differences in gene expression profiles from eight (8) muscle samples from prednisolone-treated cows and seven (7) from control animals. T-test found 64 up-regulated and 69 down-regulated transcripts in the prednisolone-treated animal group respect to the controls. In this study, we analyzed fifteen (15) bovine biceps brachii muscle samples, eight (8) from prednisolone-treated cows and seven (7) from control animals. 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.

本研究采用牛寡核苷酸微阵列（bovine oligo microarray）平台（GPL7053），对泼尼松龙（prednisolone）处理奶牛的8份肌肉样本与对照动物的7份肌肉样本的基因表达谱差异进行验证。经t检验（T-test）发现，相较于对照组，泼尼松龙处理组共存在64个上调转录本与69个下调转录本。本次研究共纳入15份牛肱二头肌（biceps brachii）样本，其中8份来自泼尼松龙处理奶牛，7份来自对照动物。基因表达谱分析基于单通道检测（single-colour detection，仅使用氰基3（Cyanine-3）），采用安捷伦-015354牛（Bos taurus）寡核苷酸微阵列平台（GPL7053）完成。微阵列使用安捷伦扫描仪G2565BA（Agilent scanner G2565BA）进行扫描，扫描参数为：左侧设置条形码，样本DNA附着于玻片背面，通过玻片玻璃完成扫描，扫描分辨率为5微米；所有玻片均在两种不同灵敏度设置（XDR高灵敏度100%与XDR低灵敏度10%）下各扫描一次。扫描仪软件将为每一组XDR扫描对生成唯一标识符（ID），并将该ID写入两张扫描图像文件中。特征提取（Feature Extraction，FE）9.5软件可通过XDR ID自动关联两组扫描图像，进而完成数据提取。经所有FE处理步骤后保留的信号为处理后信号（ProcessedSignal），该信号包含乘性去趋势、背景扣除后的信号值。