HESTA: a curated and reusable database for the human early organogenesis spatiotemporal transcriptome atlas

Abstract

BackgroundHuman organogenesis is orchestrated by precise spatiotemporal gene expression. Mapping these dynamic processes requires transcriptomic data that preserve native anatomical context across continuous developmental stages. FindingsWe present a spatiotemporal transcriptome database of human embryogenesis, profiling 77 sagittal sections from 13 euploid embryos (CS12-CS23) using Stereo-seq, yielding 14,708,858 bin50 spots. The atlas annotates 50 organs and maps 198 molecularly distinct substructures, complemented by 607,093 snRNA-seq cells. The database features a Spatial Exploration module for locating sections and visualizing spatial distributions of organs and substructures, and an Organ Atlas module for visualizing gene expression, regulon activities, and pathway enrichment at the single-organ level across stages. ConclusionsThis database provides an interactive resource to access spatial gene expression, substructures, and regulatory networks across 50 developing human organs, supporting further research into the mechanisms of human organogenesis.