Extended Data Fig. 4: Annotation of primary scATAC-seq peaks.

a, Distribution of primary scATAC-seq peaks in genomic features. b, Distribution of primary scATAC-seq peaks around transcription start sites. c, Bar plot of log(fold enrichment) of primary scATAC-seq peaks in chromatin states. Chromatin states defined by the 25-state model from Roadmap Epigenomics¹⁸ (see Methods). d, Intersection of cell-type-specific peaks (Fisher’s exact, two sided, FDR < 0.05), predicted enhancer peaks (see Methods), and peaks overlapping promoter-interacting regions identified by H3K4me3 PLAC–seq²¹. e, UMAP projections of Z-scores of enrichment of cell-type-specific peaks (Fisher’s exact, two-sided, FDR < 0.05) for each broad cell type. f, Browser tracks highlighting cell-type-specific predicted enhancers. Left, highlighting predicted enhancers linked to SOX2 in RGs that are not present in ulENs. Right, highlighting a predicted enhancer for GRIN2B that is present in ulENs and not RGs. g, h, Bar plots of −log₁₀(P) of gene ontology biological processes that are enriched in cell-type-specific predicted enhancers of MGE-derived interneurons (g) and RGs (h) (see Methods). i, Heat map of Z-scores of transcription factor motif enrichments of key lineage-associated transcription factors in each cluster.