NanoString analysis of a rat liver mRNA panel following TCDD treatment

Profiling of mRNA abundances with high-throughput platforms such as microarrays and RNA-Seq has become an important tool in both basic and biomedical research. However these platforms remain prone to systematic errors, and have challenges in clinical and industrial application. As a result it is standard practice to validate a subset of key results using alternate technologies. Similarly, clinical and industrial applications typically involve transitions from high-throughput discovery platform to medium-throughput validation ones. These medium-throughput validation platforms have high technical reproducibility and reduced sample input needs, and low sensitivity to sample-quality (e.g. for processing FFPE specimens). Unfortunately, while medium-throughput platforms have proliferated, there are no comprehensive comparisons of them. Here we fill that gap by comparing two key medium-throughput platforms – NanoString’s nCounter Analysis System and ABI’s OpenArray System – to gold-standard quantitative real-time RT-PCR.借助微阵列（microarray）、RNA测序（RNA-Seq）等高通量平台开展mRNA表达丰度谱分析，已成为基础研究与生物医学研究领域的重要工具。然而此类平台仍易受系统误差影响，且在临床与工业应用中存在诸多挑战。因此，采用替代技术对部分关键结果进行验证已成为标准操作流程。类似地，临床与工业应用通常涉及从高通量发现平台向中通量验证平台的转型。此类中通量验证平台具备较高的技术重复性，样本投入需求更低，且对样本质量的敏感度较低（例如用于处理福尔马林固定石蜡包埋（Formalin-Fixed Paraffin-Embedded, FFPE）样本）。遗憾的是，尽管中通量平台已得到广泛普及，但目前尚无针对此类平台的全面对比研究。本研究通过将两款关键中通量平台——NanoString的nCounter分析系统与ABI的OpenArray系统——与金标准定量实时逆转录PCR（quantitative real-time RT-PCR）进行对比，填补了这一研究空白。