Our precise annotation showed that, in humans, TE and ICM cells become transcriptionally distinct between the B2 and B3 stages, after the beginning of blastocyst cavitation ( Figure 1H Figure S2C). We projected all cells from our cohort of embryos on the pseudotime, linking embryo annotation to the pseudotime ( Figure 1G Figure S2C). Sample images are shown for blastocyst ID 13 (B4 stage upon scRNA-seq analysis) ( Figure 1F). We then regrouped embryos based on their position on the pseudotime ( Figure S2C). To link developmental stage and molecular events, we performed a per-embryo analysis in which cells from the same embryo were analyzed together. Our study pinpoints the precise timing of lineage specification events in the human embryo and identifies transcriptomics hallmarks and cell fate markers. We also provide evidence that NR2F2 marks trophectoderm maturation, initiating from the polar side, and subsequently spreads to all cells after implantation. We explore the dynamics of the fate markers IFI16 and GATA4 and show that they gradually become mutually exclusive upon establishment of epiblast and primitive endoderm fates, respectively. We reveal that human trophectoderm/inner cell mass transcriptomes diverge at the transition from the B2 to the B3 blastocyst stage, just before blastocyst expansion. Using time-lapse imaging of annotated embryos, we provide an integrated, ordered, and continuous analysis of transcriptomics changes throughout human development.
Here we employ pseudotime analysis of single-cell RNA sequencing (scRNA-seq) data to reconstruct early mouse and human embryo development. Understanding lineage specification during human pre-implantation development is a gateway to improving assisted reproductive technologies and stem cell research.
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