MCL-1 is required for mature TEC survival. (A) Multidimensional scaling plot comparing RNA-sequencing expression profiles for cTECs and mTECs from 1-month-old controls and Mcl1^ΔFoxn1 mice. Libraries are labeled and colored according to the genotype and TEC subset. Distances on the plot correspond to leading log 2 fold-change between each pair of samples. (B) Genes that were differentially expressed (false discovery rate < 0.05) in Mcl1^ΔFoxn1 cTECs relative to controls that are involved in TEC (red) or thymocyte (blue) development. Histograms of β5t (C), CD40 (D) expression in CD45⁻EpCAM⁺MHC II⁺Ly51⁺ cTECs and MHC I (E), CD80 (F) in CD45⁻EpCAM⁺MHC II⁺ TECs isolated from 5-week-old mice (blue and red histograms show controls and Mcl1^ΔFoxn1 mice, respectively). (G) Thymic cellularity (left) and TEC (CD45⁻MHC II⁺EpCAM⁺) numbers (right) of 4- to 7-week-old mice of the indicated genotypes. (H) Histogram of flow cytometric analysis of MCL-1 expression in CD45⁻EpCAM⁺MHC II⁺ TECs isolated from 4- to 7-week-old mice of the indicated genotypes. Data are representative of 3 independent experiments (n ≥ 2/group) (except A-F). Graph bars indicate mean ± SEM and groups were compared with a Student t test (2 sided, unpaired). **P < .01; ***P < .001; ****P < .0001.