Extended Data Fig. 1: Proportions of overarching cell types in our dataset.

(A) Different cell types are discriminable in UMAP space or by marker genes. Unsupervised Jaccard-Louvain clustering on a kNN neighbor graph delineates distinct cell types, including adaptive immune cells, monocytes, glial/neuronal cells, and erythrocytes. UMAP plots are binned in hexagons: each single hexagon represents a merged representation of all cells falling within the region. The central UMAP plot is colored by the majority cell type. Different cell types are easily distinguishable in 2-D UMAP plots. The other schex-UMAP plots show gene expression values of selected characteristic marker genes projected onto cells. The color gradient bar represents log-normalized gene expression values. Yellow represents the maximal expressed value, while purple represents the lowest expression values. Markers of distinct immune subpopulations are detected in our data: CD8 T-cells (CD8A), NK cells (GZMB), B cells (MS4A1). Similarly, different non-neuronal cells can be detected in our analysis: astrocytes (GFAP), neurons (SNAP25), and oligodendrocytes (OLIG2). Monocytes (LYZ) localize close to our microglial cells and were used for comparative expression of marker genes in Fig. 2b. Red blood cells (HBB) were also easily discriminable. (B) Microglia are the predominant cell type recovered across regions and diseases. Bar plots showing the relative representation of different cell types across different metadata parameters, with each bar summing to 100%. Overall, 95.7% of cells are microglial, 2.2% are adaptive immune, 1.5% are glial/neuronal, 0.4% are monocytic, and 0.3% are erythrocytes. The upper bar plot shows proportion of each overarching cell group across regions, while the lower plot shows the same across diseases. Mono monocytes, RBC red blood cells, LOAD late-onset Alzheimer’s disease, EOAD early onset Alzheimer’s disease, MCI mild cognitive impairment, CNTRL control, DLBD-PD diffuse Lewy body disease-Parkinson’s disease, PSP progressive supranuclear palsy, TLE temporal lobe epilepsy, MS multiple sclerosis, ALS amyotrophic lateral sclerosis, FTD frontotemporal dementia, HD Huntington’s disease, DNET dysembryoplastic neuroepithelial tumor, BA Brodmann area, AWS anterior watershed, OC occipital cortex, TNC temporal neocortex, H hippocampus, TH thalamus, SC spinal cord, SN substantia nigra, FN facial nucleus.