(A) Cell sorting strategy to obtain the EpCAM+LacZ−MHClo (P3), EpCAM+LacZ−MHChi (P2), and EpCAM+LacZ+ (P4) mTECs from the pooled thymi of Aire+/− mice. (B) Gene expression of selected epidermal markers (CK10, LEKTI, CK2–8), Aire-dependent TSAs (Ins2, MUP1, SPT1, TFF3), Aire-independent TSAs (GAD1, Csnb) and thymic chemokines (CCL19, CCL21) in the post-Aire EpCAM+LacZ+ mTECs compared with the EpCAM+LacZ−MHCIIlo and EpCAM+LacZ−MHCIIhi mTECs as measured by qPCR. The post-Aire population was characterized by a marked decrease in most of the Aire-dependent and Aire-independent genes measured, with the exception of the genes characteristic for epidermal differentiation. Data are mean ± SEM of triplicate measurement of pooled samples from 15 mice.