Extended Data Fig. 1: Quality controls and cluster characterization of brain cells in control and ALSP samples.
From: Mutations in the human CSF1R gene impact microglia’s maintenance of brain white matter integrity
a. Bar graphs of median of number of genes and median of number of UMIs of each sample sequenced in each batch. b. UMAP plot of control and ALSP samples before batch correction. c-e. UMAP plots of control and ALSP samples after batch correction by Harmony. UMAP plots are split by different samples, genders and regions respectively. f. Heatmap showing the expression of marker genes for each cell type. g. Nuclei frequencies for all cell types in each sample. For the brain regions, frontal cortex (FC), occipital cortex (OC), subcortical regions (SC), parietal and temporal lobes, basal ganglia (BG), and white matter (WM) were assessed. h. UMAP plots depicting the expression of feature genes in different cell types. i. Box plots showing average individual expression levels for CSF1R, CSF2RA, CSF3R in the myeloid cell cluster. P values were calculated by two-sided Wilcoxon rank-sum test (n = 13 controls; n = 6 ALSP). j. Scatter plot showing linear regression of average expression levels between CSF1R and CSF2RA, or CSF3R. Gray shading represents the 95% confidence interval, and Pearson’s correlation coefficient and P value are shown.
