Time course single-cell RNA-seq and single-cell ATAC-seq data from mESCs treated with retinoic acid

This study generated ~41,000 cells for scRNA-seq and ~19,000 cells for scATAC-seq from differentiating mouse embryonic stem cells over a time course. It demonstrates cRegulon method provides specific regulations of TF combinations to characterize identity and transition of cell types during retinoic acid induced mESC differentiation. Embryoid bodies from mESCs were treated with retinoic acid for up to 10 days. The EBs were collected at Day 0 (Not treated with RA), 2, 4, and 10 after treatment. Nuclei isolated from single cell were used to generate scATAC-seq data. Single cells were used to generate scRNA-seq data. The scRNA-seq library was generated using Chromium Next GEM Single Cell 3’ Kit v3.1 (10X Genomics, PN-1000268) and the scATAC-seq library was generated using Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit (10X Genomics, PN-1000175).