Transcriptome of mouse thymic and thyroid epithelial cells

We have compared the transcriptional profiles from two epithelial cell types to find genes specifically expressed in thymic medullary epithelial cells. Epithelial cells from thyroid and thymic medulla from C57BL/6 mice were sorted and their transcriptional profiles compared. Cells were gated as viable, Epcam+ CD45- for thyroid and viable, Epcam+ CD45- UEA+ for thymic medulla. Overall design: Three independent replicates were analysed per group. For Thyroid epithelial cells: 20 thyroids per replicate were minced in RPMI and digested with collagenase and DNAse. Supernatants were stained with Epcam and CD45 for FACSsort; Fluorogold was used to exclude dead cells. Thymic epithelial cells: thymi were minced, digested with collagenase, dispase and DNAse. Supernatants were stained with Epcam, CD45 and UEA for FACSsort; Fluorogold was used to exclude dead cells. Replicates 1 and 2 were from 6 pooled thymi each; replicate 3 was from 2 pooled thymi.