scRNA-seq experiments on primed mouse epiblast stem cells, blastocyst-like cell reprogramming and mouse embryonic stem cells.

Recently, a new wave of synthetic embryo systems (SESs) have been established from cultured cells toward efficient and ethical embryonic development research. We recently reported our epiblast stem cell (EPISC) reprogramming SES that generates numerous blastocyst (BC)-like hemispheres (BCLH) with pluripotent and extraembryonic cell features detected microscopically. Here, we further explored the system over key time points with unprecedented single-cell RNA sequencing (scRNA-seq) analysis and revealed broad induction of the 2C-like reporter MERVL and RNA velocity diverging three major population regions with genetic expression resembling pluripotent epiblast (EPI), primitive endoderm (PE), and trophectoderm (TE). Enrichment of those three BC-like cell fates involved key regulons, zygotic genome activation (ZGA) related genes, specific RNA splicing, and select cells meaningfully distinguished critical regulons of model cells. This analysis confirms the induction of the extraembryonic cell populations during the reprogramming and we anticipate that our unique BCLH SES and rich data may uncover new facets of cell potency, improve developmental biology, and help biomedicine advance. Overall design: Cell culture samples were prepared as approximately 3,000 single cells and then sampled for scRNA-seq 10x Genomics 3' (v3 Chemistry) library construction with standard protocol. Libraries were sequenced with paired-end reads on Illumina HiSeq X at one library per lane and then mapped to a custom reference mouse genome (mm10) using Cell Ranger (Version 3.1), including two transgenes for EGFP and mCherry involved in the related study. The related study at https://doi.org/10.1101/2020.09.29.318279