DNBSEQ-T7 Spatial transcriptomics Zebrafish App Note

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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 hours of development. We obtained 152,977 spots at a resolution of 10 × 10 × 15 μm1 with spatial coordinates. Meanwhile, we identified spatial modules and co-expressed genes for specific tissue organizations. 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. The vast sequencing data from these spatial-temporal experiments were generated by the DNBSEQ-T7 sequencer with high accuracy, low cost, and fast turnaround time.


Embryogenesis in vertebrates is an intricate and dynamic process. The zebrafish model is commonly used to study vertebrate embryogenesis. A significant challenge in deciphering embryogenesis is the lack of topographical information that can enable the correlation of cellular differentiation with environmental cues. Recent progress in sequencing technology has made it possible to assemble a single-cell atlas during the development of model organisms, thereby enabling the multi-modal information analysis of the whole genome, including the epigenetic state, RNA levels, and protein levels of a single cell.2,3 However, spatial and temporal relationships with the transcriptome states in developing zebrafish remain unknown. At present, in situ hybridization enables the exploration of expression patterns of specific genes during development but not global changes in the …

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  • Construction of the spatiotemporal
    transcriptomic atlas

    A high resolution spatiotemporal
    transcriptomic atlas of zebrafish
    embryogenesis can be constructed
    using the Stereo-seq kit S1 and the
    DNBSEQ-T7 sequencing platform.
  • Stereo-seq and DNBSEQ-T7
    provide excellent performance in
    many dimensions

    Stereo-seq chips can achieve
    true single-cell spatial resolution,
    centimeter-level panoramic field
    of view, high capture efficiency,
    and unbiased whole transcriptome

    DNBSEQ-T7 provides an ideal
    solution for spatial experiments
    with high throughput, high
    accuracy, and low cost.
  • One-stop service for rapid
    workflow and data analysis

    The Stereo-seq workflow takes
    only 8 hours from tissue sectioning
    to NGS library.

    The resulting sequencing data was
    analyzed using the ready-to-use,
    integrated bioinformatics analysis
    workflow and visualization tools.

Download the DNBSEQ-T7 Spatial transcriptomics Zebrafish App Note