Fig. 3

Gene expression signatures in NeuN⁺ and OLIG2⁺ nuclei. a Heatmap of cell type DEGs with covariates indicated. b Cell deconvolution of bulk RNA-seq data from the CommonMind Consortium and BrainSeq compared with NeuN⁺ and OLIG2⁺ (control samples). Y-axes show the weighed proportion of cells that explain the expression of bulk RNA-seq. c Gene set enrichment for cell type markers from single-nuclei RNA-seq. Enrichment analyses were performed using Fisher’s exact test. Odds ratios and FDRs (within parentheses) are shown. d Correspondence between the expression change and methylation change in cell types. The X-axis represents differential DNA methylation statistics for genes harboring DMRs in promoters. The Y-axis indicates the log₂(fold change) of expression between the two cell types. The negative correlation supports the well-established impact of promoter hypomethylation on the upregulation of gene expression