Single-cell muti-omics delineates the dynamics of distinct epigenetic codes coordinating mouse gastrulation

Our study used CoBATCH to profile the H3K27ac and H3K4me1 states in mouse embryos at six continuous developmental stages ranging from Pre-Primitive Streak to Early Headfold stages, we comprehensively analyzed two histone markers and integrative scRNA-seq query dataset. Finally, we constructed a gene regulatory network centered on pivotal transcription factors and unraveled the mechanisms of how enhancers usage coordinates the transition of gene expression along lineage progression. Overall design: The embryos were dissected at time points of E6.0, E6.5, E7.0, E7.25 and E7.5 and classified as pre-streak (Pre_Ps), Early Streak (ES), Mid-Streak (MS), Late Streak (LS), No Allantoic Bud (OB), and Early Headfold (EHF) stages according to their morphology. Embryos were digested with Collagenase I dissociation buffer at 37°C for 15-60 min to generate single-cell suspension. Single cells were subjected to single cell H3K27ac and H3K4me1 CoBATCH profiling.