Spatiotemporal mapping of gene expression landscapes and developmental trajectories during zebrafish embryogenesis
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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.
Original language | English |
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Journal | Developmental Cell |
Volume | 57 |
Issue number | 10 |
Pages (from-to) | 1284-1298.e5 |
ISSN | 1534-5807 |
DOIs | |
Publication status | Published - 2022 |
Bibliographical note
Copyright © 2022 The Authors. Published by Elsevier Inc. All rights reserved.
- Animals, Embryo, Mammalian, Embryonic Development/genetics, Gene Expression Profiling, Gene Expression Regulation, Developmental, Transcriptome, Zebrafish/genetics
Research areas
ID: 310559150