Additional file 2 of Sex-specific DNA methylation differences in Alzheimer’s disease pathology

Additional file 2: Supplementary Tables. Table S1. Sample information of the brain samples datasets included in the meta-analysis. Table S2. Quality control (QC) information on DNA methylation samples and probes for each cohort contributing to this meta-analysis. Table S3. In females, a total of 381 differentially methylated CpGs were significantly associated with the AD Braak stage at 5% FDR in the meta-analysis of four brain samples cohorts (Gasparoni, London, Mt. Sinai, ROSMAP). Table S4. In males, a total of 76 differentially methylated CpGs were significantly associated with the AD Braak stage at 5% FDR in the meta-analysis of four brain samples cohorts (Gasparoni, London, Mt. Sinai, ROSMAP). Table S5. In females, at 5% FDR, a total of 72 co-methylated DMRs were significantly associated with AD Braak stage in the meta-analysis of the four brain samples cohorts. Table S6. In males, at 5% FDR, a total of 27 co-methylated DMRs were significantly associated with AD Braak stage in the meta-analysis of four brain samples cohorts. Table S7. Enrichment of sex-specific DNA methylation changes in different genomic features. Table S8. Enrichment of sex-specific DNA methylation changes in different chromatin states. Table S9. Enrichment of sex-specific DNA methylation changes in binding sites of transcription factors and chromatin proteins assayed by ENCODE and CODEX projects. Table S10. Results of Gene Set Enrichement analysis of sex-specific CpGs and DMRs in female and males. Table S11. Significant association between sex-specific differences and expression levels of nearby genes. Table S12. The sex-specific CpGs and DMRs located within 500 kb of sex-specific SNPs associated with AD biomarkers or AD neuropathology. Table S13. mQTLs assoicated with FDR-significant CpGs in females. Table S14. mQTLs assoicated with FDR-significant CpGs in males. Table S15. mQTLs associated with significant CpGs identified by sex-by-Braak stage interaction analysis. Table S16. Sex-specific DNA methylation differences overlapped with AD drug targets in ChEMBL database. Table S17. Average beta values at each Braak stage for significant CpGs identified in female samples. Table S18. Average beta values at each Braak stage for significant CpGs identified in male samples. Table S19. Overlap of Braak-associated sex-specific CpGs and DMRs with sex-specifc DNA methylation changes in fetal development.