Extended Data Fig. 5. Gene expression and promoter epigenetic states.

a, Violin plots showing reads densities of the five histone marks in Group II-a and III-b promoters. Colors represent cell types the same as in (e). Group II-a promoters were repressed by H3K27me3 in all cell types; genes in III-b were activated by H3K27ac in neuron cells, with comparable H3K27me3 levels in all cell groups. b, Boxplots showing the expression levels of genes grouped by their promoter DNA reads densities for different histone marks. The boxes were drawn from lower quartile (Q1) to upper quartile (Q3) with the middle line denote the median, whiskers with maximum 1.5 IQR, outliers were indicated with dots. n = 2,900 genes for the first 5 groups and n = 2,898 for the 6th group of each histone modification. c, Heatmap showing the Spearman’s correlation coefficients of gene expression and promoter histone modification levels within each cell type. d, Genome browser view of aggregated Paired-Tag profiles showing the three Olfr gene clusters in chr7 was silenced by H3K9me3. e, 3D-scatter plot showing the PCA embedding of aggregated RNA profiles. PC1 differs neuron cells from glial cells and PC2 mainly separates different non-neuron cell types. f, Scatter plot showing the loadings of the first 2 PCs for each gene. Genes from group II-b and III-d were colored in brown and blue, respectively. g, UMAP embedding of 4,659 OPC and Oligodendrocytes nuclei used for pseudotime analysis. h, Expression of marker genes alone the pseudotime.