Affymetrix MOE430v2 vs Mouse PancChip 5.0 comparison

Comparison of two microarray platforms: the Mouse PancChip 5.0 and the Affymetrix GeneChip Mouse Genome 430 2.0 Array. The aim of this experiment was to determine the ability to identify differentially expressed genes in islet and pancreas RNA, and the sensitivity of the two platforms, using the same source material in a carefully controlled manner. RNA was extracted from adult mouse pancreas (n=5) and highly purified islet samples (n = 5). All samples were amplified once. 5 biological replicates (islets vs. pancreas) in a dye swap experimental design were hybridized to the PancChip. 3 biological replicates, using the same amplified RNA hybridized to the PancChip, of both the pancreas and islet samples were also hybridized to the GeneChip. All data were normalized using appropriate methods and differential expression between islet and pancreas was determined using PaGE with a 10% FDR. The study revealed that the PancChip is a highly cost effective alternative to the Affymetrix 430-2, that the PancChip is up to 60% more sensitive than the Affymetrix 430-2 GeneChip and that 80% (7,000) of the probe sets on the PancChip show expression in either Islets or Pancreas, while only 25% (6,800) show expression on the Affymetrix GeneChip.两种微阵列（microarray）平台的对比研究：小鼠PancChip 5.0平台与Affymetrix GeneChip小鼠基因组430 2.0芯片。本实验旨在通过严格受控的实验流程，使用同源实验材料，评估两种平台在胰岛与胰腺RNA样本中识别差异表达基因（differentially expressed genes）的能力，以及各自的检测灵敏度。从5只成年小鼠的胰腺组织（n=5）以及高纯度胰岛样本（n=5）中提取RNA，所有样本均进行一轮扩增。采用染料置换实验设计（dye swap experimental design）的5组生物学重复（biological replicates，胰岛vs胰腺）样本与PancChip芯片进行杂交。针对胰腺与胰岛样本，各使用与PancChip杂交实验中相同的扩增后RNA，制备3组生物学重复样本，再与Affymetrix GeneChip芯片进行杂交。所有数据均通过合适的方法进行标准化处理，采用PaGE方法并以10%的错误发现率（False Discovery Rate, FDR）作为阈值，鉴定胰岛与胰腺组织间的差异表达基因。本研究结果显示，PancChip芯片是Affymetrix 430-2芯片极具性价比的替代方案；PancChip芯片的检测灵敏度较Affymetrix 430-2 GeneChip芯片最高提升60%；PancChip芯片上80%（7000个）探针组（probe sets）可在胰岛或胰腺组织中检测到表达信号，而Affymetrix GeneChip芯片仅25%（6800个）探针组可检测到表达信号。