ZESTA: Zebrafish Embryogenesis Spatiotemporal Transcriptomic Atlas
Dataset ID: STDS0000057
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PMID:35512701
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152,977 Spots
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26,628 Genes
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Dataset information
Summary:
Vertebrate embryogenesis is a remarkably dynamic process during which numerous cell types of different lineages generate, change, or disappear within a short period. A major challenge in understanding this process 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, a high-definition spatially resolved transcriptomic technology, to dissect the spatiotemporal dynamics of gene expression and regulatory networks in the developing zebrafish embryos. We profiled 91 embryo sections covering six critical time points during the first 24 hours of development, obtaining a total of 152,977 spots at a resolution of 10x10x15 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. Our study constitutes a fundamental reference for further studies aiming to understand vertebrate development.
Technology:
Stereo-Seq
Platform:
DNBSEQ-T1
Species:
Danio rerio(danRer11)
Tissues:
Embryo
Citation:
Liu, Chang et al. “Spatiotemporal mapping of gene expression landscapes and developmental trajectories during zebrafish embryogenesis.” Developmental cell vol. 57,10 (2022): 1284-1298.e5. doi:10.1016/j.devcel.2022.04.009
Submission date: 2021-09-16Update date: 2021-09-16
Sample number: 6Section number: 91
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No results.
Accessions
Raw data: CNP0002220
Additional Data 1 (The Brightfield Image, Nucleic Acid Dye Staining Image): https://stereomap.cngb.org/zebrafish/image_staining
Additional Data 2 (The Spatially Resolved Developmental Trajectories): https://stereomap.cngb.org/zebrafish/data_index
Database: https://db.cngb.org/stomics/zesta/