BioProject

Here we report the transcriptome data of 236 single cells freshly isolated from mouse embryos on days 5. More...

Here we report the transcriptome data of 236 single cells freshly isolated from mouse embryos on days 5.5 and 6.5. Initial transcriptome data from 124 single cells yielded signature genes for the epiblast, visceral endoderm, and extra-embryonic ectoderm and revealed a unique distribution pattern of fibroblast growth factor (Fgf) ligands and receptors. Further analysis indicated that early-stage epiblast cells do not segregate into lineages of the major germ layers. Instead, some cells began to diverge from epiblast cells, displaying molecular features of the pre-mesendoderm by expressing higher levels of mesendoderm markers and lower levels of Sox3 transcripts. In addition, we identified a late stage of the day 6.5 embryo in which mesoderm and DE cells emerge, with many of them coexpressing Oct4 and Gata6. Analysis of single-cell RNA-seq data from 112 cells of the late-stage day 6.5 embryos revealed differentially expressed signaling genes and networks of transcription factors that might underlie the segregation of the mesoderm and DE lineages. Moreover, we discovered a subpopulation of mesoderm cells that possess molecular features of the extraembryonic mesoderm. This study provides fundamental insight into the molecular basis for lineage segregation in post-implantation mouse embryos. Overall design: Examination of 108 EPI cells, 8 VE cells and 8 EXE cells from 3 pregastrulation embryos (E5.5 and early-stage E6.5), and 112 cells from 3 early gastrulation embryos (late-stage E6.5). The lineages of cells were determined by Pricipal component analysis or diffusion map analysis using expression data of all genes or known markers. Less...