Single-cell RNA-seq analysis of wildtype and ETV2-overexpressing embryoid body-derived progenitor cells

Wild-type (WT) and Etv2-overexpressing (OE) mouse embryonic stem cells (mESC) were cultured and differentated to embryoid bodies (EBs) in mesodermal conditions. Induction of Etv2 in OE EBs was achieved by the addition of doxycycline. Cells were collected at different time points (i.e., D2, D3, D4 for WT and D3, D4 for OE EBs) following FACS based on the presence or absence of two surface markers: Flk1 (F+/-) and Pdgfra (P+/-). We performed single-cell RNA sequencing (scRNA-seq) on the FACS sorted cells at different time points. The transcriptomic profiles revealed that ETV2 overexpression promotes HE lineage specification while repressing cardiac and skeletal muscle programs. Overall design: A total of 13 samples were used for the capture and analysis. The following list shows the sample with the annoation format as Day_Surface-Marker_Condition: For WT EBs the samples are D2_P-F-_WT, D3_P-F-_WT, D3_P+F-_WT, D3_P+F+_WT, D3_P-F+_WT, D4_P-F-_WT, D4_P+F-_WT, D4_P+F+_WT and D4_P-F+_WT. For OE EBs the samples are D3_P-F-_OE, D3_P-F+_OE, D4_P-F-_OE, and D4_P-F+_OE.