Single-cell transcriptomic dissection of two waves of endothelial-hematopoietic transition in murine yolk sac

The yolk sac drives vertebrate embryonic hematopoiesis through primitive hematopoiesis and endothelial-to-hematopoietic transition (EHT) waves, yet dynamic cellular and molecular changes during EHT of yolk sac require elucidation. By integrating single-cell transcriptomic data from mouse embryos (E6.75-E11.0), we built a comprehensive atlas of early endothelial and hematopoietic development in yolk sac. Focusing on the yolk sac (E7.5-E9.5), we established a refined atlas capturing key cell populations of EHT in yolk sac.The repository contents:[‘merged_data.rds’] contains the Seurat Object v4 of single-cell RNA sequencing data related to Figure 1B. It includes integrated data from early whole embryo and yolk sac sampling sites. The meta.data of scRNA-seq object contains the properties of each observed cell are defined as follows: data_source: origin of raw data. location: Sampling site of mouse embryo. method: sequencing technology used for the raw data. stage: mouse embryonic developmental stages. Cluster: defines major cell types of each cell. [‘merged_yolksac.rds’] contains a Seurat Object (v4) of single-cell RNA sequencing data. This corresponds to the data presented in Figure 4A, and includes integrated data from yolk sac endothelial and hematopoietic cells. The meta.data of scRNA-seq object contains the properties of each observed cell are defined as follows: source: origin of raw data. location: Sampling site of mouse embryo. stage: mouse embryonic developmental stages. method: sequencing technology used for the raw data.batch: batch effect from different sequencing approaches and data. celltype_new: defines major cell types of each cell.