Fig. 2

Comparative analysis of single-cell microglial transcriptomes from acute and chronic neurodegeneration models unveiled a common gene regulatory signature. a-b t-SNE maps of a 944 microglial cells from FNX acute neurodegeneration in susceptibility gene-free CX₃CR1^GFP/+ mice (as in Fig. 1d-e) and b 3896 microglial cells from chronic neurodegeneration FAD model [21] based on RaceID2 transcriptomic analysis. Cells from contralateral (black square) and lesion (red square) FN and cells from wild type (WT) controls (black circle) and AD transgenic (red circle) mice are distributed uniformly in the clouds. Neurodegeneration-associated groups formed distinct tail populations (dotted circles). c Comparative differential gene expression analysis of disease-associated clusters in susceptibility gene-free FNX (orange), chronic FAD (green, [21]) and severe CK-p25 (blue; [30]) neurodegeneration models identified 72 common differentially regulated genes (red). See Table 2 and Additional file 5: Table S1 for details. d Log₂(fold-change) (y-axis) of 70 common neurodegeneration-associated genes (x-axis) identified in (c) that were similarly up- or down-regulated (represented as respective positive or negative values). Genes are categorized according to GO terms in panel titles. FNX (orange), FAD (green) and CK-p25 (blue). See also Table 2. e-h tSNE maps of common genes e H2-D1, f Axl, g Apoe, and h P2ry12 shown in (d) depict their single cell expression in the FNX and FAD data sets. Color legends represent log₂(transcript counts) across cells