Microarray development for the Grooved carpet shell clam, Ruditapes decussatus: Functional approach to host parasite interaction

An R.decussatus microarray platform was developed to to profile gene expression in R. decussatus heavy infected by Perkinsus olseni A comparative analysis of gene expression was conducted between Grooved carpet shell clam R. decussatus individuals for non infected and infected by Perkinsus olseni clam gills. Gene expression profiling was performed using an R.decussatus oligo-DNA microarray of 43,758 probes based on single-colour detection (Cyanine-3 only). Microarrays were scanned with Agilent scanner G2565BA 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.

本研究构建了欧洲缀锦蛤（R. decussatus）的基因表达微阵列平台，用于分析重度感染奥尔森派琴虫（Perkinsus olseni）的个体的基因表达谱。本研究以沟纹缀锦蛤（Grooved carpet shell clam，R. decussatus）为实验对象，针对未感染与感染奥尔森派琴虫的个体的鳃组织开展基因表达对比分析。实验采用包含43758个探针的欧洲缀锦蛤寡核苷酸DNA微阵列（oligo-DNA microarray）进行基因表达谱分析，该平台采用单通道检测模式，仅使用花青素3（Cyanine-3）进行标记。微阵列芯片使用安捷伦（Agilent）G2565BA型扫描仪完成扫描，扫描分辨率为5微米；所有芯片均以两种不同灵敏度设置（XDRHi 100%与XDRLo 10%）各扫描一次，即每片芯片完成两次扫描；扫描仪软件为每一组两次扫描生成唯一标识符，并将该标识符保存至两张扫描图像文件中。特征提取（Feature Extraction，FE）9.5软件在提取数据时，可通过XDR标识符自动将对应扫描组的两张图像进行关联。经所有特征提取处理步骤完成后得到的最终信号为处理后信号（ProcessedSignal），该信号包含乘性去趋势背景扣除信号。