ATAC-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 sorting based on the presence or absence of two surface markers: Flk1 (F+/-) and Pdgfrα (P+/-). ATAC-seq was performed using 50,000 cells and the Tn5 transposase enzyme. Sequencing of libraries was carried out on the Illumina NextSeq platform (2×50 bp). Chromatin accessibility profiling revealed that Etv2 overexpression during EB differentiation increases accessibility of genes related to the hematoendothelial lineage, while reducing accessibility of genes associated with the cardiac lineage. A total of 13 samples (each with 2 replicates) were used for the 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.