Extended Data Fig. 1: Gene expression and methylation in INTACT-isolated PV, SST, L4, and L5 neurons.

a, Representative images of Rbp4-Cre;SUN1:GFP labeling of L5 excitatory neurons and Nr5a1-Cre;SUN1:GFP labeling of L4 excitatory neurons. b, Top: marker gene expression in RNA sequencing data from each subclass profiled. Bottom: number of differentially expressed genes (DEGs) between WT cells of each subclass. c, Log2 fold-difference in gene expression between WT subclasses. The x-axis represents mean normalized counts of genes from DESeq2. d,e Log2 gene body mCA/CA calculated from bisulfite-sequencing of INTACT-isolated nuclei vs log2 gene body mCA/CA derived from pseudobulk snmC-seq⁸ data (d) or log2 gene expression TPMs from INTACT RNA-seq (e) for neuronal subclasses. ρ = Spearman’s correlation coefficient. f, Pairwise comparisons of gene body mCA/CA across subclasses. In b and f, genes enriched for expression >5 fold in one subclass over another are colored according to the subclass where they are highly expressed. For panels c-f, genes with a minimum length of 5 kb located in chromosomes 1-19 and X were analyzed to facilitate accurate mean mCA/CA calculations. Data generated from cerebral cortex tissue from 8–10-week-old MeCP2 WT and KO mice. n = 4 bioreplicates per genotype for RNA-seq, n = 2-3 bioreplicates per genotype for whole-genome bisulfite sequencing. WT and Mecp2 KO replicates were averaged for INTACT methylation calculations except d, where only WT is used to compare to WT snmC-seq data.