Spatiotemporal mapping of gene expression landscapes and developmental trajectories during zebrafish embryogenesis

Dev Cell. 2022 May 23;57(10):1284-1298.e5. doi: 10.1016/j.devcel.2022.04.009. Epub 2022 May 4.


A major challenge in understanding vertebrate embryogenesis is the lack of topographical transcriptomic information that can help correlate microenvironmental cues within the hierarchy of cell-fate decisions. Here, we employed Stereo-seq to profile 91 zebrafish embryo sections covering six critical time points during the first 24 h of development, obtaining a total of 152,977 spots at a resolution of 10 × 10 × 15 μm3 (close to cellular size) with spatial coordinates. Meanwhile, we identified spatial modules and co-varying genes for specific tissue organizations. By performing the integrated analysis of the Stereo-seq and scRNA-seq data from each time point, we reconstructed the spatially resolved developmental trajectories of cell-fate transitions and molecular changes during zebrafish embryogenesis. We further investigated the spatial distribution of ligand-receptor pairs and identified potentially important interactions during zebrafish embryo development. Our study constitutes a fundamental reference for further studies aiming to understand vertebrate development.

Keywords: Stereo-seq; embryonic development; scRNA-seq; spatial transcriptomics; zebrafish.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Embryo, Mammalian
  • Embryonic Development* / genetics
  • Gene Expression Profiling
  • Gene Expression Regulation, Developmental
  • Transcriptome
  • Zebrafish* / genetics