Extended Data Fig. 1: Characterization of SFB-tetramer+ CD4+ T cells.
a, Gating strategy used to identify SFB-tetramer+ CD4+ T cells after magnetic enrichment. Live, CD45+ single cells negative for CX3CR1, Ly6G, B220, Ly6C, MHCII and CD8 were further analysed. From the CD3+CD4+ population, SFB-specific cells were identified as double positive for APC- and PE- (Fig. 1) or single positive for APC- or PE-conjugated tetramers specific for SFB peptide QFSGAVPNKTD (all other figures). b, Mice were colonized with SFB at weaning and two weeks later thymic T cells were compared to age-matched control (CTRL) mice. Frequencies and counts of SFB-tetramer+ cells in thymic flow-through after magnetic enrichment (n = 3 per group). c, 7B8 TCR transgenic mice were left uncolonized or SFB-colonized at weaning and two weeks later CD4+ counts in the thymus were compared (control n = 6; SFB n = 7). d–f, Mice were colonized with SFB at weaning and two weeks later thymic T cells were compared to age-matched control mice. d, Frequencies and counts of SFB-tetramer+ cells in CD8+ (single-positive; SP) and CD4+CD8+ (double-positive; DP) T cells (n = 10 per group). e, Frequencies and counts of no tetramer (NT), 2W1S, H. hepaticus (HH) and human (HU) tetramer+ cells in CD4+ T cells (n = 5 per group). f, Frequencies and counts of CD4+, CD8+ and CD4+CD8+ thymic subsets. g–k, Representative flow plots of control and SFB CD4+ T cells for RORγt and FOXP3 (g), CD25 (h), CD44 (i); CD24 and TCRβ (j) and CD69 and TCRβ (k). In f–k, n = 15 per group. Each replicate is a biologically independent sample. Data are shown as individual values and mean; P values by two-tailed unpaired t-test (b, c) or two-way ANOVA with Sidak’s post hoc test (d–f).
