Fig. 2: Summary of gene expression and splicing analysis.

a Transcriptional events—exon fragments, exon-exon junctions, and exon-intron border junctions—detected at average depth per nucleotide ≥2 in T1D cases (orange), unaffected controls (CTL; blue), and in both (gray) for memory CD4⁺/CD25⁺ Tregs and memory CD4⁺/CD25⁻ T cells, and the resulting reduced transcript sets with all associated events detected. Counts and summary data are available in Supplementary Data 2. b Transcripts detected at transcripts per million (TPM) > 0 in Tregs and memory CD4⁺/CD25⁻ T cells at TPM > 0. c Genes detected at TPM > 0. Numbers of detected multi-transcript genes are presented in parentheses. The number of significantly differentially expressed genes and differentially spliced genes (FDR P < 0.05) for each cell type is displayed in red text. DE = differentially expression, DS = differentially spliced d Distribution of normalized TPM for the FOXP3 gene in memory CD4⁺/CD25⁺ Tregs (CTL: N = 35, median TPM = 96^.13, interquartile range = 74.06–123.40; T1D: N = 48, median TPM = 126.95, interquartile range = 87.99–168.15). e Distribution of mean fluorescent intensity (MFI) of the FOXP3 protein in memory CD4⁺/CD25⁺ Tregs. FC = fold change calculated as the mean type 1 diabetics (T1D) value divided by the mean control (CTL) value (CTL: N = 75, median MFI = 4187.58, interquartile range = 3676.50–4601.99; T1D: N = 78, median MFI = 4517.04, interquartile range = 4158.49–4813.18). f Exon fragment detection and gene differential exon fragment usage test for Tregs and memory CD4⁺/CD25⁻ T cells. DEFU = differential exon fragment usage. g Comparison of genes with differential exon fragment usage between Tregs and memory CD4⁺/CD25^- T cells. h Comparison of genes with differential exon fragment usage (N = 1112) and quantitatively differentially spliced genes (N = 403) in Tregs. Data for boxplots are available in Supplementary Data 3 (d) and Supplementary Data 4 (e). Upper error bars are calculated as the third quartile + 1.5× interquartile range, lower error bars are calculated as first quartile − 1.5 × interquartile range.