Fig. 3: Detection of cis-regulatory elements within the developing mouse forebrain.

a Heatmap depicting DA peaks binned along pseudotime from embryonic snATAC-Seq nuclei. DA peaks were filtered to retain only peaks that had at least one Cicero peak-peak connection. Stacked bar plots to the left of the heatmap depict the proportion of AP, BP, and N nuclei per bin. b, c Cicero connections within 0.5 Mb window centered around TSS of Lhx6 (postmitotic MGE marker), Neurod6 (postmitotic cortex marker), Nr2f2 (CGE progenitors), Sp8 (LGE progenitors), Nes (pan-AP), and Gad1 (postmitotic pan-GEs) broken down based on tissue (b) or neurogenic cell type (c). Cicero connections overlapping the TSS of selected genes are shown as purple arcs, all Cicero connections in the genomic regions are shown as orange arcs. Y-axis unit is the co-accessibility score. Only connections with co-accessibility scores greater than 0.25 are depicted. Peaks: snATAC peaks were used by Cicero to quantify peak-peak connections. Gene models are visualized at the bottom of each column with genes of interest highlighted.