Extended Data Fig. 2: Details and examples of the ‘core naïve T_reg ’ signature.

a, Schematic of the study design, describing that blood CD45RA⁺ T_conv cells, blood CD45RA⁺ T_reg cells, blood CCR8⁺ T_reg cells, skin T_conv cells and skin T_reg cells were analyzed with respect to their DNA methylation, chromatin accessibility and gene expression. Schematic generated using BioRender.com. b, UMAP showing scATAC-seq data of the analyzed cell types (encompassing 2 donors per cell type). c, Volcano plots for differential analyses on the chromatin accessibility and gene expression level (corresponding to heat maps in Fig. 2a). Features shown in red are considered statistically significant. Numbers at the top indicate the numbers of features displaying statistical significance. P values for chromatin accessibility, two-tailed likelihood ratio test (see Methods, n = 5,687 blood CD45RA⁺ T_reg cells, 6,531 blood CD45RA⁺ T_conv cells), adjusted using Bonferroni correction; P values for gene expression, two-tailed Wald test based on the raw count matrix as implemented in DESeq2, using donor ID as additional covariate (see Methods; n = 5 T_reg cell donors, 3 T_conv cell donors), adjusted using Benjamini-Hochberg correction. d, Methylation (left), chromatin accessibility (middle) and gene expression (right) of features in DMR-peak-gene links, stratified by quadrant (see Fig. 2b). Labels on the right indicate the genes in each DMR-peak-gene link. Parts of this panel are duplicated from Fig. 2a as the same features are shown. e, Methylation for selected genomic regions. Highlighted regions mark DMRs. Vertical lines at the bottom of the methylation tracks mark CpG sites. f, Smoothed methylation and chromatin accessibility for selected DMR-peak-gene links together with corresponding raw methylation for each shown CpG site (top right heat maps; rows indicate donors; columns indicate CpG sites; gray fields indicate missing values) and expression of the associated gene (bottom right bar charts; mean ± s.d.). Highlighted regions mark DMRs (methylation tracks) and differential peaks (accessibility tracks). Vertical lines at the bottom of the methylation tracks mark CpG sites. Dashed boxes mark the locations of amplicons used for validation of methylation differences. Gene expression P values, two-tailed Wald test based on the raw count matrix as implemented in DESeq2, using donor ID as additional covariate (see Methods; n = 5 T_reg cell donors, 3 T_conv cell donors) with Benjamini-Hochberg correction. Data are representative of two or more independent experiments with two or more individual donors.