Figure 6: Isolated cell populations of interest remain viable for cell culture and Next Gen RNA-sequencing.

(A) Fluorescent images of isolated cells at day 12 of cell culture. Cells are stained with fluorescent-tagged antibodies for EpCAM-PE (epithelial cell marker), CD49a-Alexa-647 (fibroblast marker), and nuclei labeled with hoechst 33342-blue. (B) Dose-response plot shows cell viability, measured by RealTime Glo luminescence, of primary epithelial cells cultured in monoculture and in co-culture with patient-matched primary fibroblasts after 72-hours exposure to docetaxel chemotherapeutic. (C) Volcano plots from cell isolation experiments show average RNA-seq transcript fold changes across 4 patients. “EpCAM-Capture vs Raw” volcano plot shows transcripts up-/down-regulated in isolated epithelial cells compared to the raw digestate (i), while “CD49a-Capture vs Raw” shows transcripts up-/down-regulated in isolated stromal cells (ii) with known epithelial and stromal markers labeled with blue dots (orange dots represent transcripts up- or down-regulated >2-fold with p-value >0.005, green dots represent transcripts up- or down-regulated >2-fold with p-value <0.005, red dots represent transcripts up- or down-regulated with p-value <0.005 but by fold change <2, and black dots represent transcripts up- or down-regulated by fold change <2 and p-value >0.005).