BulkRNA Dataset for Label-free Single Cell Phenotyping to Determine Tumor Cell Heterogeneity in Pancreatic Cancer in Real-time

FOLFIRINOX treatment remains standard of care treatment for pancreatic cancer patients. However, until now it is not completely clear whether and how the administration of FOLFIRINOX changes the molecular characteristics of the tumor, which can be an important information for following treatment strategies. Therefore, in this experimental setup, murine pancreatic cancer cells were exposed to IC50 values of FOLFIRINOX (FFX) and were afterwards recovered to mimic the clinical treatment setting. Since pancreatic cancer is also differentiated into classical (epithelial) and quasi-mesenchymal/squamous (mesenchymal) subtypes on a molecular level, murine cells with epithelial versus mesenchymal phenotypes were included to identify phenotype-specific treatment-induced patterns. Cells were afterwards sequenced to identify gene expression patterns and compared to phase images derived from digital holographic microscopy. Epithelial cells treated with FFX acquired a mesenchymal-like phenotype which remained stable even after the washout period. Interestingly, even mesenchymal cells showed increased gene expression patterns of mesenchymal markers, however not to the same extent. The RNAseq setup was used as an experimental reference method to validate phenotypic findings in digital holographic microscopy For the bulk RNA-seq experiment, six murine pancreatic cancer cell lines were analyzed, 3 epithelial lines (ID: 8442, 9592, 53631) and 3 mesenchymal llines (ID: 8081, 9091, 16992) either as controls (ctrl), after treatment for 72 hours with FOLFIRINOX (FFX) as previously described or after 72 hours washout (WOFFX) period. Triplicates were analyzed of each cell line