Extended Data Fig. 6: Characterization of AIRE-dependent mTEC subsets.
From: Single-cell mapping of the thymic stroma identifies IL-25-producing tuft epithelial cells
a, Variance of genes plotted against their mean value (genes with >50 total UMI are shown). Orange dots indicate variable genes. b, Pairwise Pearson gene correlations in AIRE-dependent (left) and AIRE-independent (right) TRA gene lists across 2,341 TEC single cells. Levels of differential expression (highest change of expression in cluster compared to median across all clusters) are indicated as bars; bar colours indicate cluster association to TEC population. c, Comparison of stochastic gene expression between Aire knockout and wild-type cells in mTEC III and IV populations. Marginal distribution is shown as histogram. Axes represent UMI count per 1,000 UMI, normalized to cell numbers. d, Flow cytometry scheme of thymic Aire knockout cells showing the percentage of each TEC population compared to wild-type percentage (shown in brackets). e, Representative immunofluorescence images of two independent experiments, for tdTomato across different organs. In the thymus, the medulla (M) and cortex (C) are separated by dashed lines, distinguished by nuclei density. Blue, DAPI. Scale bars, 100 μm. f, qPCR analysis of Csnb (left) and cre (right) genes in Csnbcre+Rosa26tdTomato (cre+) and Csnbcre−Rosa26tdTomato (cre−) across thymic populations. Dot plots display mean and error bars indicate s.e.m. n = 2 (wild type) or n = 3 (Csnbcre+) biologically independent animals. g, Flow cytometric analysis of tdTomato expression in mTEC subsets (colours as in Fig. 1) isolated from thymi of Csnbcre+Rosa26tdTomato- or Csnbcre−Rosa26tdTomato-reporter mice.
