Single-Cell Multi-omics RNA and ATAC Sequencing of In Vitro Hematoendothelial Differentiation from Mouse Embryonic Stem Cells

An in vitro differentiation system using mouse embryonic stem cells to capture multiple differentiation timepoints: days 3, 4, 5, 6, and 7 as scMultiome (ATAC+RNA) and days 0, 2, and 4 as scRNA-seq. scMultiome libraries were generated using the Single Cell Multiome ATAC + Gene Expression v1 chemistry, and scRNA-seq libraries were generated using the Single Cell 3' v3 chemistry. Nuclei isolation for scMultiome was performed using a modified 0.1X lysis protocol from 10x Genomics protocol CG000366, with the digitonin concentration adjusted from 0.001% to 0.005%.