Fig. 1: The Human Microglia Atlas (HuMicA).

a Schematic overview of the pipeline used to obtain the integrated HuMicA object. b UMAP visualization of the integrated and clustered HuMicA object, annotated by the nine obtained clusters. c Barplot representation of the number of nuclei/cells and the mean genes detected per nucleus/cell (between parentheses) in each cluster. d Dot plot representation of the expression of canonical markers of microglia (P2RY12, CX3CR1) and macrophages (MRC1, CD163) across all clusters. e UMAPs showing the module score (MSc) expression of macrophage (MRC1, CD163) markers. The gene expression values correspond to the normalized “RNA” assay of the integrated Seurat object. f Heatmap representation of the average expression values by cluster of the significant markers of all HuMicA clusters. Gene expression is represented as the z-score of the averaged normalized “RNA” counts. The number of significant markers for each cluster is represented, as well as the most significant and biologically relevant genes from each list. The dot plot represents a gene set enrichment analysis, performed using fgsea with one-tailed test, depicting the significance of the overlap between the lists of genes from the literature and the expression patterns in each HuMicA cluster. Significance is represented by the negative of the log of the adjusted p value (Benjamini-Hochberg) and the normalized enrichment score. The dots highlighted in bold are considered statistically significant (FDR < 0.05). Source data are provided as a Source Data file.