Additional file 1 of Sex dependent glial-specific changes in the chromatin accessibility landscape in late-onset Alzheimer’s disease brains

Additional file 1 : Supplementary Table 1. Demographic and sample information of all 51 patients analyzed. Supplementary Table 2. Demographic and sample information of group of 40 paired, 9 unpaired. *Donor tissue used for snRNA-seq. Supplementary Table 3. GREAT analysis of Top 5000 differential sites for Level 1 analysis. Supplementary Table 4. HOMER Motif search result of top 5000 sites more accessible in neuron and non-neuron. Supplementary Table 5. Demographic information for bulk ATAC-seq tissue samples. Supplementary Table 6. Differential analysis of Whole tissue vs neuron/non-neuron mixed. Terms in blue represent association with glial function and the ones in red represent association with neuronal function. Terms in green represent association with general brain function. GO terms enriched in DE sites of non-neuron vs whole tissue. Supplementary Table 7. GO terms enriched in DE sites of neuron vs whole tissue. Supplementary Table 8. GO terms enriched in sites more accessible in mixed neuron/non-neuron vs whole tissue. Supplementary Table 9. GO term enrichment of LOAD down differential sties in female glia controls vs. cases, FDR < 0.05. Terms in blue are associated with glial function. Supplementary Table 10. Level 1 (neuronal vs. non-neuronal) differentially accessible peaks. Supplementary Table 11. Level 2 (LOAD vs. Normal neuronal) differentially accessible peaks. Supplementary Table 12. Level 3 (LOAD vs. Normal non-neuronal female) differentially accessible peaks. Supplementary Table 13. Level 3b (LOAD vs. Normal non-neuronal female) differentially accessible peaks. Supplementary Table 14. Consistency between our snRNA-seq LOAD vs. Normal differential expression results and those of a recent publication. Our results are derived from HPCA-annotated neurons, astrocytes, and microglia. Dark orange = significantly up-regulated in LOAD, light orange = non-significantly up-regulated in LOAD, dark blue = significantly down-regulated in LOAD, light blue = non-significantly down-regulated in LOAD. Supplementary Table 15. Differential expression analysis of ROSMAP data for Level 3 female non-neuronal cells with and without covariates.