Qualitative changes in gene transcription in Smad4-deficient TECs. (A) Relationship between the average TEC and ETP frequencies in thymi from Smad4^co/co and Smad4^{co/co;Foxn1Cre} mice at different ages. Three to 5 mice per group were used at each time point. (B) Fold change of various transcripts in sorted MHCII^int () and MHCII^hi (■) TEC populations from WT mice compared with sorted MHCII^neg stroma (□). (C) Fold change of various transcripts in TEC subpopulations ( and ■) and in nonepithelial CD45^neg stroma (□) from Smad4^{co/co;Foxn1Cre} mice compared with Smad4^co/co mice. Values are means of 3 to 5 independent experiments. Bars represent SD. *P < .05, **P < .01, ***P < .005, ****P < .001.