Gene expression from laser capture microdissected epithelium and stroma during pancreatic carcinogenesis

This study used laser capture microdissection to obtain highly purified epithelial and stromal RNA samples from frozen sections of human pancreatic ductal adenocarcinoma (PDA), low-grade pancreatic intraepithelial neoplasias (PanIN) and low-grade intraductal papillary mucinous neoplasms (IPMN). Libraries were prepared using the Nugen Ovation RNA-Seq System V2 and sequenced to a depth of 30 million 100bp single-end reads. These data were used to reconstruct both an epithelial and stromal gene regulatory network of malignant pancreatic disease using the ARACNE algorithm and elucidate regulatory proteins whose dysregulation drives progression and dedifferentiation in PDA.