Food and Nutritional Genomics Research Center, Kyungpook National University, Daegu, Republic of Korea.
Biotechnol J. 2010 Sep;5(9):970-3. doi: 10.1002/biot.201000046.
Microarray analysis is an important tool in studying gene expression profiles in genomic research. Despite many concerns raised, mRNA samples are often pooled in microarray experiments to reduce the cost and complexity of analysis of transcript profiling. This study reports the results of microarray experiments designed to compare effects of pooling RNA samples and its impact on identifying profiles of mRNA transcripts and differentially expressed genes (DEGs) in the liver of C57BL/6J mice fed normal and high-fat diet. Pearson's correlation coefficient of transcripts between pooled and non-pooled RNA samples was 0.98 to 1.0. The impact of pooled vs. non-pooled RNA samples was also compared by number of transcripts or DEGs. Agreement of significant genes between pooled and non-pooled sets was fairly desirable based on t-test <0.05 and/or signal intensity ≥ 2-fold. Biological process profile and the correlation coefficiency of fold change in the hepatic gene transcripts between pooled and non-pooled samples were also higher than 0.97. This suggests that pooling hepatic RNA samples can reflect the expression pattern of individual samples, and that properly constructed pools can provide nearly identical measures of transcription response to individual RNA sample.
微阵列分析是研究基因组研究中基因表达谱的重要工具。尽管存在许多担忧，但在微阵列实验中通常会对 mRNA 样本进行pooling，以降低分析转录谱的成本和复杂性。本研究报告了设计用于比较pooling RNA 样本的效果及其对鉴定正常和高脂肪饮食喂养的 C57BL/6J 小鼠肝脏中 mRNA 转录本和差异表达基因 (DEGs) 谱的影响的微阵列实验结果。pooled 和非 pooled RNA 样本之间的转录本的 Pearson 相关系数为 0.98 到 1.0。还通过转录本或 DEGs 的数量比较了 pooled 和非 pooled RNA 样本的影响。基于 t 检验<0.05 和/或信号强度≥2 倍，pooled 和非 pooled 组之间显著基因的一致性相当理想。pooled 和非 pooled 样本之间肝基因转录本的生物学过程谱和倍数变化的相关系数也高于 0.97。这表明pooling 肝 RNA 样本可以反映个体样本的表达模式，并且正确构建的池可以提供几乎相同的转录反应测量值。
