Whole-embryo spatial transcriptomics at subcellular resolution from gastrulation to organogenesis

This dataset supports a whole-embryo investigation of the spatial and temporal regulation of gene expression during early zebrafish development. It includes high-resolution weMERFISH measurements of 495 genes at subcellular resolution across three developmental stages (50% epiboly/early gastrula, 75% epiboly/mid gastrula, and 6-somite stage/early organogenesis), together with imputed spatial expression patterns for 25,872 additional genes. For each embryo, the dataset provides cell-level transcript counts, spatial coordinates, subcellular localization of individual transcripts, and corresponding tissue and cluster annotations. In addition, the dataset contains the MERFISH-FATE cell correspondence tables that link fixed embryos to whole-embryo live imaging, enabling analysis of gene expression changes in the context of cell movements and lineage trajectories. These data collectively form a comprehensive spatial multiomics atlas of zebrafish gastrulation and early organogenesis, supporting studies of gene regulation, tissue patterning, boundary formation, and the integration of molecular and morphogenetic processes.