Pancreatic stellate and cancer cell transcriptomes from heterocellular, 3D invasive, cultures

When combined into spheres and embedded in extracellular matrix, hetero-cellular cultures of pancreatic cancer and stellate cells produce invasive, stellate-led, projections. In order to establish what cancer and stellate cells are expressing in this context we generated chimeric spheres of mouse and human cells. Invasive spheroids could then be processed for RNA sequencing, with reads mapped back to parent species and thus cell type. Overall design: Two sets of human (Miapaca2 and Panc1) and mouse (DT6066, R254) pancreatic cancer cells were combined with mouse and human pancreatic stellate cells, respectively, and formed into hetero-cellular spheres. Spheres were then embedded in collagen : matrigel hydrogels and cultured for 72 hours at which point invasive projections are evident. Total RNA was obtained through Trizol extraction and processed for sequencing. Cell type specific information was then extracted my matching reads to host species and therefore cell type.