This study investigates the transcriptional dynamics of mouse organogenesis at single-cell resolution using sci-RNA-seq3, a method that profiles ~2 million cells from 61 mouse embryos staged between 9.5 and 13.5 days of gestation. The resulting 'mouse organogenesis cell atlas' (MOCA) provides a comprehensive view of developmental processes during this critical window. The authors identify hundreds of cell types and 56 trajectories, many of which are detected due to the depth of cellular coverage. They define thousands of marker genes corresponding to each cell type and explore gene expression dynamics within cell types using Monocle 3. The study reveals marked changes in cell type proportions during organogenesis and characterizes the apical ectodermal ridge, a specialized epithelium involved in digit development. The authors also reconstruct developmental trajectories, identifying ten major trajectories that span all major systems, including the CNS, PNS, respiratory, digestive, cardiovascular, immune, lymphatic, urinary, endocrine, integumentary, skeletal, muscular, and reproductive systems. The study highlights the potential of single-cell atlases for understanding mammalian development and the role of specific genes and regulatory sequences in developmental processes.This study investigates the transcriptional dynamics of mouse organogenesis at single-cell resolution using sci-RNA-seq3, a method that profiles ~2 million cells from 61 mouse embryos staged between 9.5 and 13.5 days of gestation. The resulting 'mouse organogenesis cell atlas' (MOCA) provides a comprehensive view of developmental processes during this critical window. The authors identify hundreds of cell types and 56 trajectories, many of which are detected due to the depth of cellular coverage. They define thousands of marker genes corresponding to each cell type and explore gene expression dynamics within cell types using Monocle 3. The study reveals marked changes in cell type proportions during organogenesis and characterizes the apical ectodermal ridge, a specialized epithelium involved in digit development. The authors also reconstruct developmental trajectories, identifying ten major trajectories that span all major systems, including the CNS, PNS, respiratory, digestive, cardiovascular, immune, lymphatic, urinary, endocrine, integumentary, skeletal, muscular, and reproductive systems. The study highlights the potential of single-cell atlases for understanding mammalian development and the role of specific genes and regulatory sequences in developmental processes.