Comparison of ectopic gene expression in Cdx1+/+ and Cdx1-/- thymic medullary epithelial cells

We have found that Cdx1 can promote ectopic gene expression in thymic epithelial cells. We isolated MHCIIhi CD80hi medullary thymic epithelial cells from Cdx1-/- and Cdx1+/+ and compare gene expression between the two subsets, also in the context of Cdx1-mediated changes in intestinal epithelial cells. Three independent replicates were analysed per group. For thymic epithelial cells: thymi were minced, digested with collagenase, dispase and DNAse. Supernatants were stained with anti-Epcam, anti-CD45, UEA1, CD80 and MHCII for FACSsort; Fluorogold was used to exclude dead cells. Replicates were pooled from material from 4-6 thymi. For small intestine, cells from 3 mice were pooled per replicate.