Extended Data Fig. 1: Runx1 transcript is expressed in MHC-II^low mTECs.

a, Relative expression of Runx1 mRNA in stromal cells. Downloaded from the Immgen expression database. b, qPCR of Runx1 gene expression in sorted MHC-II^high and MHC-II^low mTECs and Ly51⁺ cTECs from Foxn1-Cre (-)/Runx1^fl/fl (Cre(-)) and Foxn1-Cre(+)/Runx1^fl/fl (Cre(+)) mice. c, qPCR of Runx1 gene expression in sorted single positive (SP) CD4⁺ thymocytes, SP CD8⁺ thymocytes, double positive (DP) CD4⁺/CD8⁺ thymocytes, splenic CD4⁺ T cells, splenic CD8⁺ T cells, and splenic CD19⁺ B cells. d, Confocal microscopy of cytokeratin 5 (KRT5) (red) and cytokeratin 8 (KRT8) (green) from 30-day old thymi. Images taken at 63X magnification. Scale bars = 5 μm. Data are representative of three independent experiments. e, Flow cytometry (left) and percentage (right) of MHC-II^high cTECs gated on CD11c⁻/CD45⁻/EpCAM⁺/Ly51⁺/UEA-1⁻/IA^b+ TECs (n = 5 mice; two independent experiments). f, Flow cytometry (left) and percentage (right) of Ki67⁺ cTECs gated on CD11c⁻/CD45⁻/EpCAM⁺/Ly51⁺/Ki67⁺ TECs (n = 5 mice; two independent experiments). g, Flow cytometry and percentage/absolute number of positively selected T cells gated on TCRβ and CD69 (n = 3 Cre(-) and n = 5 Cre(+) mice; two independent experiments). (e-g) In graphs, the bars correspond to the mean, with error bars showing ±SD of values shown, and each data point represents an individual mouse. (e-g) P values by unpaired two-tailed t-test.

Source data