Human Embryogenesis Spatiotemporal Transcriptomic Atlas

I. Database Overview

The Human Embryogenesis Spatiotemporal Transcriptomic Atlas provides a spatial and temporal atlas of gene expression in human embryos at early gestation, which is critical for understanding embryo development, organogenesis, and disease origins.

Using Stereo-seq, we obtained the spatiotemporal transcriptome from 77 sagittal sections of 13 human embryos at Carnegie stages 12–23 (CS12–CS23). We established the development trajectories and regulatory profiles of 50 organs, and identified the top organ-specific regulons with the highest scores as potential organ-identity regulators. The atlas refines the key organs and cell types that are vulnerable to virus infection and genetic disorders. We found dynamic changes of imprinting gene expression in specific organs at different stages. Our work, for the first time, revealed the time-lapse and spatial transcriptome dynamics of human embryogenesis after gastrulation.

The database consists of the following main sections:

Spatial Explorer: Spatial visualization of clustering and 3D reconstructions

Organ Atlas: Organ-centric gene, pathway and regulon activity maps

Single-cell: Single-cell RNA-seq visualization

Analysis: Cross-dataset gene search, allele visualization, comparison visualization

Download: Data and metadata download

II. Spatial Explorer – Spatial Visualization

The Spatial Explorer module provides interactive spatial visualizations of sections, clusters and 3D reconstructions.

1. Embryo Overview

   Embryo Overview page serves as the visual gateway to the spatial data, providing an intuitive overview of where each section originates within the intact embryo. It bridges macroscopic anatomy with microscopic spatial transcriptomics.

2. Spatial Clustering

   Visualizes organ-level spatial clustering annotations for each section.

   Supports interactive operations such as zooming, panning and selecting clusters.

   Displays cluster annotations and metadata on the interface.

3. Substructure Clustering

   Visualizes substructure-level clusters within each section.

   Allows exploration of fine-grained anatomical regions and their marker genes.

4. 3D Reconstruction

   Shows 3D reconstruction of a representative embryo sample.

   Supports rotation, zooming, and sectioning in the 3D view.

III. Organ Atlas – Organ-centric Multi-omics

The Organ Atlas module provides organ-centric views of gene expression, pathway activity and regulon activity across organs and developmental stages.

1. Organs – Gene

   Organ-specific spatial gene expression maps.

   Each dataset is represented as an m bin50 × n genes matrix, where each value is the expression level of a gene in a bin50 region.

   Users can select organs and genes to visualize spatial expression patterns and compare across stages.

2. Organs – Regulon

   Organ-centric spatial regulatory network visualization.

   To infer spatial regulatory networks for each organ substructure:

   The merged raw count matrix was first subsampled to optimize computation.

   Regulatory networks were inferred using Stereopy with method=KNN.

   Regulon activity was quantified by AUCell enrichment scores, yielding an m bin50 × n regulons matrix describing per-bin50 regulon activity.

   The AUCell matrices were converted to h5ad files for interactive visualization.

3. Organs – Pathway

   Organ-centric spatial pathway activity maps.

   To quantify pathway activity:

   The R package irGSEA was used to perform rank-based gene set enrichment analysis on the merged raw count matrix.

   The UCell algorithm was applied to compute per-bin50 enrichment scores against Gene Ontology (GO) Biological Process gene sets.

   The resulting m bin50 × n pathways matrix of enrichment scores was compiled into h5ad files for interactive visualization.

IV. Single-cell – Single-cell RNA-seq Visualization

The Single-cell module provides visualization of matching single-cell RNA-seq datasets.

Supports UMAP/t-SNE plots and cell-type annotation.

Users can explore gene expression across clusters and compare with spatial maps in Organ Atlas.

V. Analysis – Cross-dataset Analysis Tools

The Analysis module provides several tools for cross-dataset and cross-species analysis.

1. Gene Overview

   Search for genes to view spatial maps across dataset sections.

2. Cross-Species Comparison

   Compare spatial gene expression between two datasets (e.g., different stages, organs or species).

3. Allele

   Visualizes the spatial expression distribution of genes with significant allelic imbalance.

   Users can select different sections and use the dropdown list to select genes with significant allelic imbalance expression, displaying their spatial expression distribution on the section.

VI. Download – Data and Metadata Access

The Download page provides access to the data associated with this atlas.