Fig. 2

Proportions of LOAD and normal nuclei among cell types and subtype clusters. a and b, Uniform manifold approximation and projection (UMAP) dimensional reduction plots of (a) snRNA-seq and (b) snATAC-seq datasets split into LOAD and normal groups following integration and clustering of the total nuclei population. Cell types are labeled in top plots and cell subtype clusters are shown in center plots. Lower plots show distribution of donor samples within subtype clusters (see also Additional file 1: Figure S2). c, Box plots quantifying differences in proportion of nuclei from each donor belonging to each cell type (number of nuclei from a particular donor belonging to a particular cell type divided by total number of nuclei for the same donor) split by diagnosis, based on snRNA-seq dataset. As indicated, plots represent cell datasets following QC filtering and without QC filtering. Dots represent means for each sample set. Boxes represent interquartile range, with median values indicated via horizontal line. Mean values are indicated by open diamonds. Whiskers extend to sample means within 1.5 times the interquartile range. Asterisks represent statistical significance of variation between LOAD and normal mean values at FDR-adjusted p-value levels of FDR < 0.05 (*), FDR < 0.01 (**) and FDR < 0.001 (***) based on bootstrapped Wilcoxon test. d, Box plots quantifying differences in cell type proportions between LOAD and normal samples based on snATAC-seq dataset. e and f, Box plots quantifying differences in subcluster proportions between LOAD and normal samples based on (e) snRNA-seq and (f) snATAC-seq datasets