Fig. 2

Cultured microglia recapitulate the transcriptomic profiles of CNS myeloid cells in a range of conditions. A recent meta-analysis by Friedman et al. of multiple microglia gene expression datasets revealed co-regulated gene modules expressed by myeloid cells in a variety of conditions. The extent to which these co-regulated modules could describe the heterogeneity of in vitro microglia was tested by treating each module as a gene set and calculating the percentage of UMIs in each cell that originated from each gene set. a Proliferation genes are cell cycle genes that are expressed by actively dividing microglia and are strongly enriched in cluster 6. b The macrophage gene set contains unique markers of brain macrophages when compared to parenchymal microglia and is expressed at low levels in almost every cluster, though most strongly concentrated in clusters 0 and 6. c The Interferon related gene set contains genes upregulated as part of the interferon signaling pathway and is expressed at low levels in parts of cluster 4. d The LPS related gene set contains genes that respond to LPS stimulation and is expressed at low levels in many clusters, most strongly in cluster 4. e Markers that uniquely characterize monocytes compared to microglia and other macrophages make up the Monocyte gene set, and are expressed by a subset of cells in clusters 3 and 4. f The resting microglia gene set contains homeostatic microglia markers that uniquely define microglia and is expressed in clusters 1,2, and 5. g Activation markers of microglia seen in a variety of neurodegenerative disease are contained in the Neurodegeneration module. There is robust neurodegeneration expression across all clusters, highlighting the heightened activation profile of cultured microglia, and the signal is strongest in cluster 1. h Heatmap showing the average scaled gene set percentage of each cluster allow the classification of Seurat clusters into specific module-related classes