During SLAS (Lab Automation) 2009 we presented a low cost, automation friendly, screening platform that used reporter gene assays (RGA’s) to delineate the interaction of small molecules with canonical mammalian signal transduction pathways. Our experience with this approach over the last decade has demonstrated its broad utility in the support of phenotypic screening, ranging from generating mechanism of action hypotheses for individual compounds to characterizing compound libraries. Furthermore, this RGA panel inspired and guided the development of additional platforms that are more comprehensive and flexible in terms of both cell types under investigation and the scope of biological activity detected. This presentation will focus on several of these new technologies, which all leverage Next Generation Sequencing technologies in order to measure RNA expression levels in a multiplexed fashion. The suite of approaches provide users with the ability to balance sequencing depth, transcriptome coverage and cost per well in their assay design. Coupled with internally designed automation platforms these systems allow expression levels of thousands of genes to be monitored in every well of an HTS-sized screen.