Extended Data Fig. 3: ScRNAseq quality control and cell clustering.
From: Single-cell and spatial RNA sequencing identify perturbators of microglial functions with aging
a) Graphs show the distribution of cells from scRNAseq by the number of total unique genes (left), by the number of Unique Molecular Identifiers (middle), and by percent mitochondrial content (right). b) Graph shows the top 2000 variable features with the top 20 labeled. c) UMAP plots of 15411 cells from 4 experimental groups: PBS or OxPC injected spinal cords from 6wk or 52wk old mice. Left plot shows an overlay of cells based on origin, PBS injected 6wk mice (purple), PAzePC injected 6wk mice (blue), PBS injected 52wk mice (green) or PAzePC injected 52wk mice (red). Right plot shows the separation of cells from each experimental group into 20 clusters. d) Graph showing the total number of cells from each experimental group. Significance indicated as * p < 0.05, ** p < 0.01, one-way ANOVA with Tukey’s multiple comparison comparing the treatments against each other. Data are represented as mean ± SD. e) Graphs showing the number (left) and percent (right) of non-mononuclear phagocytes (MPH) cell clusters from each experimental group. f) Dot plot shows the expression of various cell lineage signature genes across the 20 cell clusters. MPH clusters selected for downstream analysis are highlighted by green dashed lines. The size of the dot corresponds to the percentage of cells expressing the gene in each cluster. The colour represents the average gene expression level. Sample size n = 3 per experimental group (each n represents a pool of 4 spinal cords for a total of 12 mice per group) and data are represented as mean ± SD.
