Research applying single-cell analysis techniques and comparisons to a cell atlas resource allowed researchers at the Babraham Institute to connect observed development defects caused by disrupted DNA methylation processes with an understanding of the cell types affected. This work, published in Genome Biology, builds on previous work undertaken with collaborators to establish a detailed cell atlas charting cell fate through early development. This work contributes important new knowledge to understanding the role of DNA methylation during embryogenesis, helping decipher the rules that govern how different cell types arise. An understanding of these rules will be essential for researchers to be able to accurately and safely direct cell fate to produce clinically-relevant cell types for regenerative medicine.