Extended Data Fig. 9: mTEC IV shape the thymus immune niche.

a, Heat map showing a metacell analysis of 3,500 CD45⁺IL-25R⁺ cells across five clusters. b, Differential gene expression in ILC2 cells from two biological replicates compared to other CD45⁺IL-25R⁺ cells (rest) from each replicate. Axes represent log₂ fold change. c, Percentages of CD45⁺ cells in Pou2f3 knockout and wild-type thymi, determined by flow cytometry. Circles and diamonds indicate independent mice, centre line indicates the mean value. d, Flow cytometry analysis of cells expressing CD4, CD8, CD25 and CD44 in Pou2f3 knockout and wild-type thymi. The experiment was repeated independently four times with similar results to confirm reproducibility. e, Flow cytometry sorting scheme of thymic CD45⁺IL-25R⁺ cells from Pou2f3 knockout and wild-type thymi. f, Percentage of CD45⁺IL-25R⁺ cells in Pou2f3 knockout and wild-type thymi. Circles and diamonds indicate independent mice, centre line indicates the mean value. g, Percentages (left) and numbers (right) of ILC2 (Lin⁻TCR⁻CD127⁺GATA3⁺Rorγt⁻) cells within the single-cell gate in Pou2f3 knockout and wild-type mice. Circles and diamonds indicate independent mice, centre line indicates the mean value. A one-tailed Student’s t-test was used for the comparison, *P < 0.05.