Transcriptome of mouse epithelial cells

We have compared the transcriptional profiles from three epithelial cell types to find common and differentially expressed genes. Epithelial cells from small intestine and kidney from C57BL/6 mice were sorted and their transcriptional profiles compared. Cells were gated as viable, Epcam+ CD45- for kidney, and viable, Epcam+ CD45- MHCIIhigh for small intestine MHCIIhi and viable, Epcam int CD45- MHCII low for small intestine MHCIIlo. Three independent replicates were analysed per group. Kidney epithelial cells: kidneys were minced, digested with collagenase, dispase and DNAse. Supernatants were stained with Epcam and CD45 for FACSsort; Fluorogold was used to exclude dead cells. Small intestinal epithelial cells: small intestines were cut open, contents removed and minced. Fragments were washed and incubated with EDTA, and supernatants were stained with Epcam, CD45 and MHCII; Fluorogold was used to exclude dead cells. For small intestine, cells from 3 mice were pooled per replicate. For Kidney, cells from 4 mice were pooled per replicate.