Extended Data Fig. 3: Microglial proportions across individual donors and donor-region pairings.

(A) Proportions of microglial subtypes across single donors. Proportions of microglial subtypes are plotted by donor, with selected metadata annotated in a header bar above. Each bar represents a single donor and sums to 100%. Samples are clustered hierarchically based on proportions of each subtype. Donors have variability in the exact proportions of different subtypes but exhibit consistent amounts of the most common subtypes in our dataset, clusters 1 through 6. (B) Proportions of microglial subtypes across region-donor pairings. Samples are aggregated to donor-region pairings (for example, AD1-BA9) to give a proportion of different clusters for each region for each individual. Boxplots are computed for specific region-disease pairings showing the median (center), 25% (left hinge), and 75% (right hinge), for the proportion of cells across all samples for which that combination of disease and region was sampled. Whiskers represent 1.5 IQR from the nearest hinge, and outliers are not shown, nor are minima or maxima. Proportions are shown on the x-axis, and the scale varies depending on the cluster in question. [Number of independent samples per category: TNC_TLE (6), TNC_PSP (1), TH_MS (2), SN_PSP (1), SN_LOAD (3), SN_DLBD-PD (5), SN_CNTRL (1), SC_ALS/FTD (2), SC_ALS (9), OC_TLE (1), OC_Stroke_lesion (1), Lesion_MS (1), H_TLE (2), H_PSP (1), H_LOAD (14), H_HD (1), H_FTD (1), H_EOAD (2), H_CNTRL (1), FN_ALS (4), DNET_DNET (1), BA9_Stroke_lesion (1), BA9_PSP (1), BA9_MS (2), BA9_MCI (4), BA9_LOAD (35), BA9_HD (1), BA9_FTD (1), BA9_EOAD (2), BA9_DLBD-PD (5), BA9_CNTRL (1), BA9_ALS/FTD (2), BA9_ALS (8), BA4_CNTRL (1), BA4_ALS/FTD (2), BA4_ALS (9), BA20_LOAD (9), BA20_HD (1), BA20_EOAD (2), AWS_MS (2), AWS_MCI (3), AWS_LOAD (13)].