Expression profiling of rat heart and blood after amiodarone treatment. Rattus norvegicus

In the present study, an oligonucleotide microarray platform was used to compare expression profiles of heart and blood in rats treated with amiodarone against respective controls. Male Sprague-Dawley (CD) rats, which were 10 weeks old and weighed 290-320 grams at the beginning of the study, have been treated for ten days with amiodarone by oral route at a dose of 300mg/Kg/die. The study has been constituted by a control group, which received the vehicle (methylcellulose 1%, w/v), and by a treatment group (10 animals for both groups). For each tissue sample, total RNA has been individually extracted and evaluated. For each tissue, three pools/group (2 pools composed of 3 animals and the last one by 4) have been used for microarray analysis. A modulation of 600 genes in heart and 8300 genes in blood has been obtained. Overall design: In this study, we analyzed the gene expression profiles of 6 pools (3 composed of control rats and 3 composed of rats treated with amiodarone) for each tissue (blood and heart) using the Agilent-014879 Rat oligo microarray platform (12 arrays, no replicates) 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 creates a unique ID for each pair of XDR scans and saves it to both scan image files. Feature Extraction 9.5 uses XDR ID to link the pairs of scans together automatically when extracting data. The signal remaining, after all the FE processing steps have been completed, is ProcessedSignal that contains the Multiplicatively Detrended, Background-Subtracted Signal. The heart and blood samples were normalized separately.

本研究采用寡核苷酸微阵列（oligonucleotide microarray）平台，对比经胺碘酮（amiodarone）处理的大鼠心脏与血液的基因表达谱，并以相应对照组作为参照。本研究选用的雄性斯普拉格-道利（Sprague-Dawley, CD）大鼠在实验开始时周龄为10周，体重介于290~320克，通过口服途径以300mg/kg/日的剂量接受胺碘酮处理，持续10天。实验分为对照组与处理组，每组各10只动物；对照组给予赋形剂（1%甲基纤维素水溶液，w/v），处理组给予胺碘酮。针对每份组织样本，均单独提取总RNA（total RNA）并进行质量评估。每组组织设置3个混合样本池：2个混合池各包含3只动物，剩余1个混合池包含4只动物，所有混合样本池均用于微阵列分析。实验结果显示，心脏组织中共计600个基因出现表达调控，血液组织中则有8300个基因出现表达调控。整体实验设计：本研究针对心脏与血液两种组织，各使用6个混合样本池（3个来自对照组大鼠，3个来自胺碘酮处理组大鼠），采用基于单色检测（仅使用花青素3（Cyanine-3））的安捷伦-014879大鼠寡核苷酸微阵列平台（共12张芯片，无重复）进行基因表达谱分析。微阵列扫描使用安捷伦G2565BA扫描仪（Agilent scanner G2565BA），扫描时将条码朝向左侧、DNA探针面朝向背侧，透过玻片完成扫描，扫描分辨率为5微米；所有玻片均以两种不同灵敏度设置（XDRHi 100%与XDRLo 10%）各扫描一次；扫描仪软件会为每一组XDR扫描对生成唯一标识符，并将该标识符保存至两张扫描图像文件中。特征提取软件9.5（Feature Extraction 9.5）可通过该XDR标识符自动关联两组扫描数据，完成数据提取。经过特征提取软件的全部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信号（Multiplicatively Detrended, Background-Subtracted Signal）。心脏与血液样本分别进行归一化处理。