Extended Data Fig. 5: Characterization of RNA-seq and ATAC-seq clusters by cluster.

a, Expression specificity of genes in each RNA-seq cluster as in Fig. 2c, for each individual cluster. Box and midline: 25th, 50th and 75th percentiles; whiskers: 1.5 interquartile range from box. b, Analyses of ATAC peak clusters as in Fig. 2e and H-K, for each individual cluster. Boxplot as in a. c, Overlap between individual RNA-seq and ATAC clusters. Color scale for top-right panel: odds ratio, Fisher’s exact test, only results with odds ratio >1, BH corrected P value ≤0.001, and more than 50 overlapping regions are shown. d, Overlap between individual DNAme and ATAC clusters. Color scale for top-right panel: odds ratio, Fisher’s exact test. e, Fraction of DMRs in the ATAC clusters that are dynamic versus static over time as in as in Fig. 2f, for each ATAC cluster. f, Overlap of early and late shared ATAC clusters with DNAse I hypersensitivity sites in a panel of tissues and cell types from the ENCODE database, by tissue. g, Percentage of overlapping ATAC-seq regions for each bulk ATAC-seq cluster for CPN and CThPN (y axis) with genomic features derived from E14 whole mouse brain and adult cortex H3K27ac and polymerase 2 ChIP-Seq from ENCODE as well as enhancers defined by CAGE-Seq from the FANTOM5 consortium (x axis), excluding all ATAC-Seq regions overlapping with annotated Ensembl promoters.