Gastrulation is the fundamental process in all multicellular animals through which the basic body plan is first laid down^1,2,3,4. It is pivotal in generating cellular diversity coordinated with spatial patterning. In humans, gastrulation occurs in the third week after fertilization. Our understanding of this process in humans is relatively limited and based primarily on historical specimens^5,6,7,8, experimental models^9,10,11,12 or, more recently, in vitro cultured samples^13,14,15,16. Here we characterize in a spatially resolved manner the single-cell transcriptional profile of an entire gastrulating human embryo, staged to be between 16 and 19 days after fertilization. We use these data to analyse the cell types present and to make comparisons with other model systems. In addition to pluripotent epiblast, we identified primordial germ cells, red blood cells and various mesodermal and endodermal cell types. This dataset offers a unique glimpse into a central but inaccessible stage of our development. This characterization provides new context for interpreting experiments in other model systems and represents a valuable resource for guiding directed differentiation of human cells in vitro.

原肠胚形成是所有多细胞动物的基本过程，通过该过程首先制定基本的身体计划^1,2,3,4 。它对于产生与空间模式协调的细胞多样性至关重要。在人类中，原肠胚形成发生在受精后第三周。我们对人类这一过程的理解相对有限，主要基于历史标本^5,6,7,8 ，实验模型^9,10,11,12或最近的体外培养样本^13,14,15,16 。在这里，我们以空间分辨的方式描述了整个原肠胚人类胚胎的单细胞转录谱，分期为受精后 16 至 19 天。我们使用这些数据来分析存在的细胞类型并与其他模型系统进行比较。除了多能外胚层之外，我们还鉴定了原始生殖细胞、红细胞以及各种中胚层和内胚层细胞类型。该数据集提供了对我们发展的中心但难以进入的阶段的独特视角。这种表征为解释其他模型系统中的实验提供了新的背景，并为指导体外人类细胞定向分化提供了宝贵的资源。