Assessment of a highly multiplexed RNA sequencing platform and comparison to existing high-throughput gene expression profiling techniques [3pDGE]

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: 3' Digital Gene Expression (3'DGE) for immortalized human bronchial epithelial cells (AALE) exposed to chemical and genotypic perturbations

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Reed E, Moses E, Xiao X, Liu G, Campbell J, Perdomo C, Monti S