Assessment of a highly multiplexed RNA sequencing platform and comparison to existing high-throughput gene expression profiling techniques [microarray]. Assessment of a highly multiplexed RNA sequencing platform and comparison to existing high-throughput gene expression profiling techniques [microarray]

In this study, we report the performance of one such technique denoted as sparse full length sequencing (SFL), a ribosomal RNA depletion-based RNA sequencing approach that allows for the simultaneous sequencing of 96 samples and higher. We offer comparisons to well established single-sample techniques, including: full coverage Poly-A capture RNA-seq and microarray, as well as another low-cost highly multiplexed technique known as 3’ digital gene expression (3’ DGE). Data was generated for a set of exposure experiments on immortalized human lung epithelial (AALE) cells in a two-by-two study design, in which samples received both genetic and chemical perturbations of known oncogenes/tumor suppressors and lung carcinogens. SFL demonstrated improved performance over 3’ DGE in terms of coverage, power to detect differential gene expression, and biological recapitulation of patterns of differential gene expression from in vivo lung cancer mutation signatures. Overall design: Microarray RNA expression for immortalized human bronchial epithelial cells (AALE) exposed to chemical and genotypic perturbations

本研究报道了一种被称为稀疏全长测序（sparse full length sequencing, SFL）的技术的性能表现，该技术是一种基于核糖体RNA消减的RNA测序方法，可同时对96份及更多样本进行测序。本研究将该技术与数种公认成熟的单样本技术进行了对比，包括全覆盖Poly-A捕获RNA测序、基因芯片，以及另一种名为3'端数字基因表达谱（3’ digital gene expression, 3’ DGE）的低成本高多重复用技术。本研究采用二乘二实验设计，针对永生化人肺上皮（AALE）细胞开展了一系列暴露实验，所有样本均接受了已知致癌基因/抑癌基因与肺癌致癌物的遗传与化学扰动，并由此生成了相关数据集。相较于3'端数字基因表达谱，稀疏全长测序在覆盖度、差异基因表达检测效能，以及对体内肺癌突变特征对应的差异基因表达模式的生物学重现性等方面均展现出更优性能。整体实验设计：对经化学与基因型扰动处理的永生化人支气管上皮（AALE）细胞进行基因芯片RNA表达检测。