Quantitative Analysis of Musashi2-reporter positive and Musashi2-reporter negative KPf/fC pancreatic cancer cell transcriptomes

Purpose: The goal of this study is to compare the transcriptome of pancreatic cancer stem cells (Musashi2-reporter positive) to pancreatic cancer non-stem cells (Musashi2-reporter negative). Methods: Musashi2-reporter mice contain a GFP-cassette knocked into the first exon of the endogenous Musashi2 locus; heterozygous mice are used to track cells expressing Musashi2. These mice were crossed to the KPf/fC (Ptf1a-Cre; KrasG12D; p53f/f) mouse model of pancreatic cancer. Tumors from endstage Musashi2-reporter KPf/fC mice were dissociated and FACS sorted for EpCAM+/GFP+ (Musashi2+ stem cells) and EpCAM+/GFP- (Musashi2- non-stem cells). For sequencing, mRNA libraries were generated from total RNA and sequenced with 50 basepair (bp) single end reads (SR50) to a depth of approximately 30 million reads per sample on an Illumina HiSeq2500 using V4 sequencing chemistry. Conclusions: Our study provides comparative transcriptomic data from primary isolated pancreatic cancer stem and non-stem cells in biologic replicates. KPf/fC pancreatic cancer stem (Musashi2+) and non-stem (Musashi2-) cell mRNA profiles from late-stage primary tumors were generated by deep-sequencing biological triplicates using Illumina HiSeq2500.