Extended Data Fig. 3: Detailed view of astrocyte LMRs, NSC LMRs and expression of intersecting genes.
From: DNA methylation controls stemness of astrocytes in health and ischaemia
a-b, Heatmaps of LMR methylation (left) and expression of intersecting genes (right) in pseudotime. a, All significant LMRs which intersect a gene. b, Labeled LMRs from Fig. 3a. Note that some genes intersect multiple LMRs. Rows are ordered by hierarchical clustering of gene expression values. Cells are separated by tissue and then binned in pseudotime. c, Detailed view of DNA methylation near Slc1a2 in pseudobulk samples of each cell state. Each CpG is represented by a colored vertical line representing its average methylation value in the pseudobulk sample. Short black lines denote the position of CpGs with sequencing coverage. Colored purple/red bars denote LMRs. d-e, Log-normalized expression of Slc1a2 and mean methylation of LMRs intersecting this gene. f-h, Same visualization for Efnb2. For expression and methylation of additional NSC / astrocyte markers, see Supplementary Figs. 4–6. i-j, Chromatin accessibility of naive wild-type cells. i, Average promoter (TSS ± 1 kb) accessibility of genes up- or downregulated in the NSC lineage. To minimize the impact of outliers on the color scale, the 1% (methylation) or 5% (accessibility) highest and lowest values are clipped. j, Mean chromatin accessibility of astrocyte LMRs and NSC LMRs, as well as the difference between these two means (bottom, analogous to the methylome score).
