MOE430 whole mouse - mouse colon dilution series - RMA preprocessed. Mus musculus

This data is part of a large-scale platform comparison experiment. Whole mouse and adult mouse colon RNA was mixed at different concentrations (100:0, 75:25, 50:50, 25:75, and 0:100) and distributed across multiple centers for analysis. Eight microarray platforms and RT-PCR were tested for different labeling protocols, amplification protocols, and data preprocessing approaches in order to maximize data intercomparability. The role of universal reference RNA was also examined. Probes of different platforms were matched using gene symbols and/or RefSeq/GenBank accession numbers. Several different normalization procedures were applied. Evaluation criteria included linearity, sensitivity/specificity, and reproducibility within and between platforms, labeling methods, and laboratories. Keywords: dilution series Overall design: Whole mouse (sacrificed on day 1, strain: C57BL/6) and adult mouse (8 weeks, strain: C57BL/6 ) colon RNA from multiple animals was pooled respectively. RNA was purified following the manufacturer’s recommendations and integrity was analyzed using an Agilent BioAnalyzer 2100 according to manufacturer instructions. Five RNA samples were created by mixing the two original samples at different concentrations (100:0, 75:25, 50:50, 25:75, and 0:100). The five master mix samples were then divided into duplicate sets of the five sample RNAs, distributed to individual laboratories, and hybridized to eight different microarray platforms at several different genome centers. The five samples included here were prepared from 10ng of total RNA using a T7 double amplification protocol as described in Schwab et al., 2003 and hybridized to Affymetrix MOE430 arrays as recommended by the manufacturer using the standard protocol. No replicates were produced.

本数据集隶属于一项大规模平台对比实验。将全小鼠RNA与成年小鼠结肠RNA以不同浓度比例（100:0、75:25、50:50、25:75及0:100）混合后，分发至多所中心开展分析。本次实验共测试了8种微阵列平台（microarray platform）与逆转录聚合酶链式反应（RT-PCR），并针对不同标记方案、扩增方案及数据预处理方法开展验证，以最大化不同数据集间的可比性；同时还考察了通用参考RNA的作用。不同平台的探针通过基因符号（gene symbol）及/或RefSeq/GenBank登录号进行匹配。本次实验采用了多种归一化处理流程。评估指标涵盖线性度、灵敏度/特异性，以及不同平台、标记方法与实验室内部及彼此间的重现性。
关键词：梯度稀释系列（dilution series）
整体实验设计：分别将全小鼠（于第1天处死，品系：C57BL/6）与8周龄成年小鼠（品系：C57BL/6）的多只个体结肠RNA混合制备样品。RNA纯化流程严格遵循厂商推荐方案，并依照操作手册使用安捷伦生物分析仪2100（Agilent BioAnalyzer 2100）检测RNA完整性。通过以不同浓度比例混合两种原始RNA样品，共制备得到5份RNA样本（浓度比例同上）。随后将这5份混合母液样本分为两组重复样本，分发至各合作实验室，并在多个不同的基因组中心针对8种不同微阵列平台完成杂交实验。本次提供的5份样本均以10ng总RNA为起始量，采用T7双重扩增方案（T7 double amplification protocol，参照Schwab等2003年的研究）制备，并依照厂商推荐的标准流程在Affymetrix MOE430阵列（Affymetrix MOE430 array）上完成杂交。本数据集未设置重复样本。