A high-temporal-resolution single-cell transcriptomic atlas of pre- to post-implantation transition in mouse embryogenesis

Embryo implantation is a pivotal phase in early mammalian embryonic development. However, the mechanisms guiding the embryos from pre- to post-implantation remain largely elusive. Here, we present a comprehensive transcriptomics atlas of mouse embryo implantation, characterized with high temporal resolution. We collected mouse embryos at distinct stages— before, during, and after implantation— and performed single-cell RNA sequencing. Our analysis of 22,171 single-cell transcriptomes elucidates the developmental trajectories encompassing the entire implantation process. Overall design: we collected mouse embryos from pre-to post-implantation stages at E3.5, E4.5, E4.75, E5.0, E5.25, and E5.5 for single-cell RNA sequencing (scRNAseq) with the 10x genomics protocol.