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Identifying genetic and genomic characteristics that determine the functional or phenotypic properties of individual tissues and cells in multicellular organisms is a fundamental problem in modern biology. While high-throughput techniques, such as RNA-seq, are indispensable tools, they are most often performed on bulk tissue samples and inherently blur the properties of individual cells within a heterogeneous tissue. The authors present the CellRaft® Technology as a method that provides two key advantages over existing single cell isolation approaches for genomics: selective isolation without the requirement for a pre-selection step, and the ability to sort cells based on complex temporal or spatial phenotypes or cellular markers. To evaluate this approach, CFPAC-1 cells were plated on CellRaft™ Arrays and treated with 0, 2, or 5 nM gemcitabine and allowed to grow on the array for 4 days, with strongly restricted growth seen in the cells treated with 5 nM gemcitabine. Cells of interest, either proliferative or non-proliferative, were subsequently isolated and sequenced, thereby linking a proliferative pancreatic cancer cell phenotype, in the presence of a chemotherapeutic agent, to the altered transcriptome of the cells.