Fig. 3

H3K27ac ChIP-seq analysis of PD and control samples. a Different peak-sets used for the different stages of ChIP-seq analysis. Shown, as an example, is a genomic region around the oligodendrocyte marker MBP. Peaks annotated to this region, in each peak-set are shown by colored boxes. The CellType_peak-set was used for the MSP calculation. Group specific peak-sets were used to characterize the distribution of H3K27ac bound regions in cases and controls. Barplots show the comparison between the two groups (Supplementary Table S3). PD group exhibited higher number of peaks, higher percentage of unique peaks and higher percentage of genomic coverage, consistent with genome-wide H3K27 hyperacetylation. The PW_peak-set was used for the differential peak analysis. Shown are group overlays of sample fold of change compared to input control. b Hierarchical clustering of the samples indicated that samples cluster based on their cellular composition. Supplementary Fig. S6 shows the association of each of the variables with the main principal components of the data. c MA plot based on the PW_peak-set indicates that increased H3K27ac in PD is observed genome-wide, rather than being restricted to specific regions. d Manhattan plot showing the distribution of genomic locations and differential p-values of the H3K27ac PW_peak-set. The red dashed line indicates the -log10 of the highest p-value with < 5% false positive rate (Benjamini-Hochberg adjusted p-value < 0.05). Corresponding plots for the NBB cohort are shown in Supplementary Fig. S5