Extended Data Fig. 5: Summary of the human cortical biopsy microglial dataset and LIGER alignment with iMGL dataset. | Nature Immunology

Extended Data Fig. 5: Summary of the human cortical biopsy microglial dataset and LIGER alignment with iMGL dataset.

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

Extended Data Fig. 5

a) UMAP projection of cluster annotations of human brain biopsy (BB dataset) single dataset from ref. 29. b) UMAP projection, cells colored by patient. c) UMAP projection (as in a) number of genes (nGene, left) and number of unique molecular identifiers (nUMI, right). d-f) UMAP projection (as in a), cells colored by expression of CX3CR1, C1QA, P2RY12, TREM2 (d), GPNMB and LPL (e), HLA-DRA and HLA-DRB1 (f). g) Proportion of cells across joint clusters for each dataset (iMGL or brain biopsy dataset). h-k) UMAP projection LIGER integration of iMGL or brain biopsy dataset, cells colored by datasets (iMGL top, brain biopsy bottom) for expression of GPNMB (h), MX1 (i), MKI67 (j), CX3CR1 (k, iMGL left, brain biopsy right). l) UMAP projection (as in h), brain biopsy cells only with the BB_CRM_CCL3 state highlighted. m) Heatmap of the relative enrichment significance of positively enriched marker genes from each in vivo human microglial cluster from ref. 24, within differentially expressed genes of each iMGL cluster (GSEA analysis). n) UMAP projection (as in h) of cells from iMGL dataset only colored by substrates or untreated.

Back to article page