CD4^LNGFR.FOXP3 cells partly maintain the Treg signature after adoptive transfer on day 50 of life. All of the transcriptomic data came from a single experiment in which CD4^LNGFR.FOXP3 cells, CD4^LNGFR cells, and WT Tregs were isolated from the corresponding treated mice (respectively; n = 4, n = 2, and n = 2) euthanized at 50 days old. (A) A volcano plot (the fold change [FC] vs the P value) of the transcriptomes of CD4^LNGFR.FOXP3 vs CD4^LNGFR cells on day 50. The murine Treg-upregulated signature (in red), downregulated signature (in blue),²⁴  and murine core Treg gene annotations are highlighted.²⁵  The values in the top half represent the number of corresponding Treg signature genes induced (right) or repressed (left), with the number of upregulated signature genes in red and the number of downregulated signature genes in blue. P values for the Treg signature enrichment were obtained in a χ² test. (B) A heat map showing expression of the core Treg genes.²⁵  The values correspond to the FC for each gene in each sample, normalized against the mean value for CD4^LNGFR cells. (C) The Treg signature score for the murine core Treg genes²⁵  in CD4^LNGFR.FOXP3 cells, where 0 and 1 correspond to expression in Tconvs (CD4.LNGFR) and Tregs, respectively. The mean plus or minus SD signature score for CD4^LNGFR.FOXP3 cells is represented. (D) A heat map showing all of the significant differentially expressed genes (absolute FC > 2; P < .05) when comparing CD4^LNGFR.FOXP3 cells with CD4^LNGFR cells (n = 677). The log10 FC for the 3 groups of mice is shown. The Treg-downregulated signature belongs to the most downregulated genes (green). Most of the upregulated genes are involved in the cell cycle (GO:007049; false discovery rate < 0.001) whereas the most upregulated genes in both Tregs and CD4^LNGFR.FOXP3 came from the Treg-upregulated signature (red). The gene names are given beside each group.