The impact of proinflammatory cytokines on the β-cell regulatory landscape provides insights into the genetics of type 1 diabetes

This dataset contains DNA methylation profiles generated using the Infinium MethylationEPIC BeadChip (Illumina, 850K). DNA was extracted from endocrine cell (EC) cultures that were either exposed or unexposed to the pro-inflammatory cytokines IL-1β and IFN-γ for 48 hours (n = 5 biological replicates per condition). DNA extraction was performed using the QIAamp DNA Mini Kit (QIAGEN), and 1 µg of DNA per sample (10 samples in total) was processed for array hybridization and scanning following Illumina’s standard protocols. Raw array data were preprocessed and analyzed using the RnBeads R package (v3.2.0). Differential methylation between cytokine-treated and control samples was assessed using empirical Bayesian hierarchical linear models implemented in the limma package (v3.40.0). Analyses were performed on M values (log-transformed β values). P-values were adjusted for multiple testing using the Benjamini–Hochberg false discovery rate (FDR) correction. CpG sites were considered differentially methylated if they exhibited an FDR-adjusted p-value < 0.05 and an absolute β-value difference > 0.2 (≥ 20% methylation change). A full list of differentially methylated CpGs is provided in Supplementary Table 7 of the associated publication.