Supplementary Figure 9: Assessment of regional differences in human microglia phenotypes by probability binning using the antibody Panel B. | Nature Neuroscience

Supplementary Figure 9: Assessment of regional differences in human microglia phenotypes by probability binning using the antibody Panel B.

From: Human microglia regional heterogeneity and phenotypes determined by multiplexed single-cell mass cytometry

Supplementary Figure 9

The top panel shows the same tSNE map of concatenated FCS files (n = 36 biologically independent samples). The coloring in (a) indicates nine donors and five brain regions (left and right plot, respectively, legends shown in (e)), (b) overall cellular density of the concatenated files (left plot, spectrum from blue, low density, to red, high density) with a superimposed binning grid (512 bins) and unadjusted P-values (right plot) of bin-wise Skillings-Mack test for frequency differences between five brain regions, and (c) unadjusted p-values in differentially abundant hyperspheres (using cydar/edgeR framework), overlaid onto the tSNE map. The testing was performed on n = 35 independent huMG samples (SVZ (n = 8); THA (n = 8); CER (n = 5); GTS (n = 8) and GFM (n =6)) from 8 biologically independent donors. (d) tSNE plots of concatenated FCS files of each brain region. (e) Heatmap representing the pairwise earth mover’s distances (EMD) between cellular density distributions over the tSNE-space among all huMG samples. Hierarchical clustering highlights samples that have a similar phenotype, as indicated by low EMD values (top left colour bar).

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