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. Overall design: 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).