Fig. 1: Chromatin accessibility in the mouse embryonic forebrain is cell type and state-specific.
From: An epigenome atlas of neural progenitors within the embryonic mouse forebrain
a Schematic of snATAC-Seq workflow and neurogenic cell types: apical progenitors (APs), basal progenitors (BPs), and posmitotic neurons (Ns). b–e UMAP visualization of single nuclei clustered by brain region (b), SLM (c), neurogenic cell type (d), and pseudotime (e). In d, promoter accessibility (PA) representing reads mapping within 2 kb upstream of TSSs. f–m PA scores for genes enriched in specific neurogenic cell types (f–i) or distinct brain regions (j–m). n–q Aggregated reads per SLM cluster. Nkx2-1 (MGE), Neurod6 (cortex), Nes (APs), and Dcx (BPs/Ns), arranged by either brain region (n, o) or neurogenic cell type (p, q). The y-axis range for chromatin accessibility tracks are normalized to the maximum reads per gene. Peaks: differentially accessible peak coordinates, H3K4me3: H3K4me3 signal from E12.5 forebrain ENCODE ChIP-Seq data.
