Extended Data Fig. 3 |. m⁶A landscape analyses of human islets treated with IL-1β and IFN-α reveal differential methylation of class I MHC-mediated antigen processing and presentation genes (related to Fig. 3).

a, Venn diagram representation of the m⁶A hypermethylated, m⁶A hypomethylated, upregulated, or downregulated genes in human islets treated with IL-1β and IFN-α compared to PBS. Statistical analyses were performed using the Benjamini-Hochberg procedure and genes were filtered for FDR<0.05. b-e, Pathway enrichment analyses of m⁶A hypermethylated and upregulated (a), m⁶A hypermethylated and downregulated (c), m⁶A hypomethylated and upregulated (d), or m⁶A hypomethylated and downregulated genes (e) in human islets treated with IL-1β and IFN-α compared to PBS. P values were calculated according to the hypergeometric test based on the number of physical entities present in both the predefined set and user-specified list of physical entities. f, MHC class I differentially m⁶A methylated genes in human islets treated with IL-1β and IFN-α compared to PBS. g, Protein-protein interactions network of class I MHC-mediated antigen processing and presentation differentially m⁶A methylated in human islets treated with IL-1β and IFN-α compared to PBS. h-j, Coverage plots of m⁶A peaks ERAP1in human islets treated with IL-1β and IFN-α or PBS (h) (n = 15 biological independent samples/group), EndoC-βH1 cells treated with IL-1β and IFN-α or PBS (i) (n = 6 independent experiments/group), or human T1D and Control islets (j) (Controls, n = 20; T1D, n = 7 biological independent samples). Plotted coverages are the median of the n replicates presented. All samples in each panel are biologically independent. P values of pathway enrichment analysis were calculated according to the hypergeometric test based on the number of physical entities present in both the predefined set and user-specified list of physical entities. Source numerical data are available in source data.