Fig. 1

Single-cell epigenomic profiling of mouse gastrula. A: Schematic of the experimental design. Single cells from the embryonic portion of Pre_PS to EHF mouse embryos were collected and subjected to CoBATCH to profile H3K27ac and H3K4me1 states at single-cell levels. The area below the dashed line indicates the sampling location (embryonic portion). Colors represent morphological landmarks during gastrulation. ES to MS: Yellow delineates the extent of the embryonic mesoderm. LS: Light blue marks the node at the distal tip; pink indicates the posterior amniotic fold (not yet fused to the anterior proamniotic fold). OB: Blue denotes the head process extending anterior to the dorsal tip (now visible); green marks the small allantois. EHF: Blue indicates head fold formation; green represents the enlarged allantois. B and C: UMAP showing the clustering of single cells from H3K27ac (B) and H3K4me1 (C) profiles, respectively. D-G: Stacked bar plots showing the percentage of each cell stage (D, E) and cell type (F, G) identified by H3K27ac (D, F) and H3K4me1 (E, G) single-cell ChIP-seq across different developmental stages. Pre_PS, Pre-Primitive Streak; ES, Early Streak; MS, Mid-Streak; LS, Late Streak; OB, No Allantoic Bud; EHF, Early Headfold