Fig. 3

Identifying new epigenomics-induced subpopulations by simultaneously analyzing transcriptomic and epigenomic profiles in mouse kidney. a UMAP visualization of cells, which are colored by the inferred subpopulations. b Heatmap of differentially expressed genes. For each cluster, the top 10 marker genes and their relative expression levels are shown. Selected genes for each cluster are color-coded and shown on the right. c UMAP plots show the cell cluster-specific patterns of the identified factors (left), and the ranking plots show the top marker genes in the corresponding factors (right). In the projected factor pattern plots, cells are colored based on the loading values in the factor from the inferred cell loading matrix. In gene ranking plots, genes are ranked based on the gene scores in the factor from the gene loading matrix. Labeled genes are representative markers. d Heatmap showing the relative chromatin accessibility of cluster-specific loci. e Heatmap of the raw chromatin accessibility of individual cells (left) and the average chromatin accessibility of cell clusters (including C2, C7, C8, and C10) (right) using differential accessible loci among the cell clusters. f Regulatory information of eight identified cell clusters. The identities of these subpopulations were shown on the most left