Shen Sophie, Werner Tessa, Chiu Han Sheng, Chen Xiaoli, Nguyen Quan, Palpant Nathan J
Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD, 4067, Australia.
Sci Data. 2025 Jul 15;12(1):1238. doi: 10.1038/s41597-025-05549-w.
Human pluripotent stem cells offer a scalable platform to study genetic and signalling mechanisms governing cell lineage decisions during differentiation. Genome-wide and single-cell transcriptomics technologies likewise offer high-throughput analysis of heterogeneous cell differentiation states. While in vivo development has been extensively characterised using these technologies, there remains a need for comprehensive single-cell transcriptomic profiling of stem cell differentiation from pluripotency. Understanding gene expression changes governing differentiation in vitro is key to developing high fidelity differentiation protocols and understanding fundamental mechanisms of development. We generated a single-cell RNA sequencing time course to study the role of developmental signalling pathways on multilineage diversification from pluripotency in vitro. The combined dataset of over 60,000 cells spans cell types from a time course of differentiation across all germ layers, ranging from gastrulation cell states to progenitor and committed cell types. These data provide a diverse benchmarking reference point to compare against in vivo development and advance understanding of signalling regulation of differentiation, providing insights into protocol development, drug screening, and regenerative medicine applications.
人类多能干细胞提供了一个可扩展的平台，用于研究在分化过程中控制细胞谱系决定的遗传和信号传导机制。全基因组和单细胞转录组学技术同样提供了对异质细胞分化状态的高通量分析。虽然利用这些技术已经对体内发育进行了广泛的表征，但仍需要对从多能性开始的干细胞分化进行全面的单细胞转录组分析。了解体外控制分化的基因表达变化是开发高保真分化方案和理解发育基本机制的关键。我们生成了一个单细胞RNA测序时间序列，以研究发育信号通路在体外从多能性进行多谱系分化中的作用。超过60000个细胞的组合数据集涵盖了从原肠胚形成细胞状态到祖细胞和定向细胞类型的所有胚层分化时间序列中的细胞类型。这些数据提供了一个多样化的基准参考点，可与体内发育进行比较，并促进对分化信号调节的理解，为方案开发、药物筛选和再生医学应用提供见解。
