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, supportin..., , # Whole-embryo spatial transcriptomics at subcellular resolution from gastrulation to organogenesis

Dataset DOI: [10.5061/dryad.j0zpc86v9](https://doi.org/10.5061/dryad.j0zpc86v9)

## Description of the data and file structure

weMERFISH data, containing single-cell measured and imputed gene expression, and subcellular localization data of individual transcripts. This dataset includes whole-embryo spatial transcriptomics measurements for 495 genes acquired at subcellular resolution across three zebrafish developmental stages, together with imputed spatial expression patterns for 25,872 additional genes generated through integration with single-cell multiome data. For each embryo, the dataset provides cell-level transcript counts, 3D spatial coordinates, transcript-level subcellular positions, and tissue and cluster annotations.

The repository also contains the MERFISH-FATE correspondence tables that link fixed embryos to whole-embryo live imaging, enabling exploration of gene expressi...,