HeliScopeCAGE-based DGE analysis. (A) A multidimensional scaling (MDS) plot for replicate HeliScopeCAGE-based DGE data shows distance of samples based on tag distribution in expressed genes. (B) Differential gene expression between pRA+Treg and the indicated T-cell types. Numbers indicate the number of significantly upregulated genes in either cell type (5% false discovery rate cutoff) for each pairwise comparison. Boxes contain generic gene ontology (GO) terms (color coding refers to the corresponding cell type, numbers in parentheses correspond to enrichment q values) enriched in each differential gene set. A complete list of all expressed genes and corrected q values for all relevant pairwise comparisons is provided in supplemental Table 3. (C) DGE data for the top 50 significantly differentially expressed genes in a pairwise comparison of pRA+Treg vs pRA+Tconv. Shown are data for both primary and expanded RA+ cells. (D) A Treg core signature displaying unsupervised hierarchical clustering of genes differing highly significantly in expression between pTreg and pTconv in both CD45RA⁺ naïve and CD45RA^– memory subpopulations. eTreg were included in the clustering to visualize expression changes of core Treg genes after in vitro expansion. Values were log₂ transformed and normalized to the geometric mean of tag counts in pTreg and pTconv subpopulations for every gene.