Extended Data Fig. 9. Visual cortex layer 2/3 sublayer-specific genes are targets of MeCP2 regulation.

a, Characteristics of visual L2/3 excitatory neuron sublayer type-specific genes defined by Cheng et al., 2022³, showing long gene length, high numbers of intragenic cCREs and enriched mCA. ****p < 0.0001 two-sided Wilcoxon rank-sum test. b, Heatmap showing overlap and significance of excitatory neuron sublayer type-specific genes defined by Cheng et al., 2022³ with core MeCP2-regulated gene lists. Numbers in the tiles represent enrichment (log2 odds ratio) of core MeCP2-regulated genes in each L2/3 gene list. c, Heatmap of MERFISH-quantified expression for excitatory neuron sublayer type-specific genes defined by Cheng et al.³ in IT excitatory neurons in L2/3 of MeCP2 KO/+ V1 (top). d, Heatmap showing overlap and significance of excitatory neuron sublayer type-specific genes defined by Cheng et al.³ with genes detected as significantly dysregulated in pseudobulkDGE analysis of MERFISH data in excitatory neurons in sublayer depth quintiles of L2/3 of the V1. Numbers in the tiles represent enrichment (log2 odds ratio) of L2/3 genes in dysregulated gene lists of the excitatory neurons in each sublayer depth quintile of L2/3 of V1.

n=3 biological replicates for MeCP2 KO/+ MERFISH across 4 imaged brain sections.