Organoids derived from pancreatic adenocarcinoma patients share morphological and genetic features with the primary tumor [Drop-seq]

In this study, we applied Drop-seq, a high throughput single cell RNA-seq platform, to characterize the different cell types present in pancreatic cancer organoids. We sequenced the transcriptomes of 7675 single cells from organoids derived from a patient undergoing a Whipple procedure for pancreatic ductal adenocarcinoma (PDAC). We then developed a novel clustering approach based on a class of probabilistic generative models called topic models, leading to the identification of subpopulations of cells. Overall design: Dropseq of organoids derived from patient 1. Mature organoids were pooled, made into single cell suspension and 17 single cell RNAseq libraries were generated starting from 15 separate dropseq runs.