Expression data from human pancreatic cancer cell lines and mouse orthotopic tumors generated using human PDAC cell lines replete and depleted for RBFOX2

RBFOX2 is an RNA binding protein that directs alternative splicing. In this study, we characterized RBFOX2-mediated alternative splicing in pancreatic cancer (PDAC) In this dataset, we assayed gene-level and exon-level expression differences in pancreatic cancer cell lines replete and depleted for RBFOX2 expression and in 8 pairs of orthotopic pancreas tumors and related liver metastases generated from human 4039 or Panc1 cell lines replete or depleted for RBFOX2. 3 human PDAC cell line pairs replete (NTC) and depleted (KD) for RBFOX2 with no biological replicates were analyzed for differential gene expression and exon usage on a population level, comparing KD vs.NTC. Gene-level and exon-level data for human genes expressed in the population of orthotopic pancreas tumors generated using RBFOX2 depleted human 4039 or Panc1 cell lines was compared with gene-level and exon-level data for human genes expressed in the population of RBFOX2 replete orthotopic pancreas tumors generated using 4039 or Panc1 cells (KD vs. NTC). Array data from matched liver metastases and from two unmodified cell lines with low RBFOX2 expression were included in the normalization.