ABSTRACT One of the recurring questions that continues to pique the interest of academics and clinicians is to understand the functional, transcriptional, and epigenetic programs of rare cells often implicated in tumor recurrence, neurological disorders, chronic infections, and other diseases. Massively parallel single cell genomic tools can partially address this market need; however, the scientific community has made it clear that digital transcript counting is insufficient, and there is strong pull for instruments that provide more comprehensive, multi- dimensional single cell datasets. In particular, there is a need for high-throughput single cell phenotyping tools, which has lagged behind genomics tool development due to the increased difficulty of working with live cells. To meet this demand, Celldom is developing a platform that combines image-based phenotyping with single cell transcriptomics at the massive scales necessary to measure both live cell function and gene expression at the desired endpoint. We achieve this convergence by utilizing efficient microfluidic trap arrays patterned with locally printed DNA barcodes, which allows us to both take images of single cells and prepare barcoded scRNA-seq libraries of the same cells. Building on the solid progress in our Phase I award, in which we demonstrated that the steps in our workflow are all technically feasible and compatible, which include the ability to print DNA barcodes inside sealed microfluidic chips, trap single cells in an array, acquire high-resolution images of each cell, and finally prepare cDNA libraries from barcoded primers attached to surfaces, in this Phase II, we will unify this workflow and demonstrate the ultimate goal of deploying our approach in a drug discovery platform that combines time lapse imaging and high-resolution transcriptome analysis of single cells. Our work plan is summarized in three specific aims. Our first aim is to show that thousands of uniquely barcoded PCR primers can be printed inside our chips in one unique primer per chamber format, and that these chips can be used in the preparation of high quality scRNA-seq libraries with low chamber cross-contamination. Our second aim is to demonstrate that this transcriptomics workflow can be successfully implemented after extended duration in vitro cell culture, during which time the barcodes are continually exposed to enzymes present in the serum and any extracellular secretions. Our third aim is to show that knowledge of the specific barcodes allows the transcripts derived from specific chambers to be selectively enriched during the pooled amplification steps – this will be used to demonstrate targeted sequencing of high-priority clones, which is of particular interest to our target customers. After all three aims have been individually demonstrated, they will be combined in a final demonstration showing the ability to identify drug-resistant clones and probe their transcriptomic signatures at high ...