Transcriptomic analsyis of Epithelial and Mesenchymal carcinoma cells using the nCounter PanCancer Immune Profiling panel (Nanostring Technologies) [mouse]

We undertook to determine whether carcinoma cells residing in the epithelial or quasi-mesenchymal phenotypic states differ in their expression of immunomodulatory markers. To do so, we used the nCounter PanCancer Immune Profiling Panel (Nanostring Technologies)to perform transcriptomic analyses of the E and qM mammary carcinoma cells; these cells were either cultured in vitro or prepared by FACS sorting of GFP-labelled carcinoma cells from their corresponding tumors RNA was extracted from the indicated cell lines cultured in vitro or from sorted GFP+ tumor cells using the RNeasy Mini Kit (Qiagen) and transcriptomic analysis was performed using the nCounter PanCancer Immune Profiling Panel (Nanostring Technologies) Normalization of Nanostring nCounter gene expression values and differential expression were assayed by DESeq2. SnailLO cells express low levels of endogenous Snail and high levels of Epcam. SnailHI cells express high levels of Snail and low levels of Epcam.