Author Spotlight: A Pipeline to Analyze Lineage-Specific Mutant Embryos at Single-Cell Resolution

We focus on deciphering the mechanisms controlling early cell fate decisions during embryonic stem cell differentiation, both in vitro and in mouse models. Complex regulatory networks guide differentiation during development, and we investigate how the interplay of signaling pathways, transcription factors, and epigenetic regulators promote different cell fates. Studying the dynamic and rapid process of gastrulation in mice is technically challenging due to the small number of cells per embryo and the limited number of embryos with the desired genotype per litter.

While literature extensively shows the study of single cells using wild type or fluorescent-activated cell sorted populations of embryos, a comprehensive analysis of embryos with lineage mutations is still limited. Our protocol offers the possibility of generating single-cell omic datasets from gastrulating embryos harboring lineage mutations. It will help scientists with none or limited mouse handling experience or who wanna learn early embryo manipulation or single-cell approaches.

Our protocol will help answer new scientific questions in gastrulation and early organogenesis, including heart development. We provide a pipeline to analyze lineage-specific mutant embryos at single-cell resolution, which will facilitate analysis of the role of a specific genes in lineage commitment. We hope to use this methodology to understand the regulatory mechanisms of cell fate decisions during the rapid and dynamic process of gastrulation.