Extended Data Fig. 3: Annotation and gene expression signatures of iMGL datasets. | Nature Immunology

Extended Data Fig. 3: Annotation and gene expression signatures of iMGL datasets.

From: Exposure of iPSC-derived human microglia to brain substrates enables the generation and manipulation of diverse transcriptional states in vitro

Extended Data Fig. 3

A) Heatmap illustrating the relative GSEA enrichment significance of positively enriched marker genes from each microglial cluster from xenotransplanted iMGLs in vivo26, within all differentially expressed genes for each iMGL cluster. b) UMAP projection of iMGL dataset, cells colored by cell cycle phase (G1, G2M and S) c) UMAP projection of iMGL dataset, cells colored by module scores of transcriptional signature identified in xenotransplanted iMGLs in vivo26. d) UMAP projection of iMGL dataset, cells colored by expression of LPL, GPNMB (iMGL_2 and iMGL_8), HLA-DRA, HLA-DRB1 (marker genes for iMGL_3, iMGL_4 and iMGL_7), MX1, IFIT3 (marker genes for iMGL_11), TOP2A or MKI67 (marker genes for iMGL_6, iMGL_9, iMGL_10). e) Heatmap of the top 100 (top) or top 5 (bottom) differentially expressed genes for each iMGL cluster. f-h) Upset plots (left) summarizing the number of unique and shared differentially expressed genes for each cluster within each microglial state identified and heatmaps (right) showing the expression of positively enriched genes for the constituent clusters of each state. i) Upset plots (as in g) for clusters iMGL_1, iMGL_5 and iMGL_11.

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