Transcriptomic profile of embryoid bodies under hypoxia at single cell level

Abstract

Oxygen availability is a key regulator of cellular physiology and hypoxia plays a central role driving vasculogenesis and angiogenesis during development. While bulk transcriptomics has revealed important oxygen-regulated gene networks, such approaches cannot resolve the cellular heterogeneity and lineage dynamics characteristic of early differentiation. To address this, we generated a single-cell transcriptomic dataset from murine embryoid bodies, a widely used in vitro model of early embryonic development, cultured 8 or 10 days under hypoxic (1% O2) or normoxic (21% O2) conditions for the final 16 or 48 hours of differentiation. This resource enables detailed exploration of how oxygen availability influences lineage specification, vascular and hematopoietic development, and cellular heterogeneity during early differentiation. Beyond developmental biology, the dataset provides a valuable reference for comparative studies of hypoxia responses, benchmarking of single-cell analysis methods, and integrative investigations into oxygen signaling across diverse biological systems.