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Related Experiment Video

Updated: Sep 19, 2025

Spatially Compact Arrangement of Larval Zebrafish Sections for Spatial Transcriptomic Analysis
07:40

Spatially Compact Arrangement of Larval Zebrafish Sections for Spatial Transcriptomic Analysis

Published on: May 16, 2025

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Spatially Compact Arrangement of Larval Zebrafish Sections for Spatial Transcriptomic Analysis.

Jacob Buford1, Owen Wilkins2, Fred Kolling2

  • 1Department of Surgery, Dartmouth Hitchcock Medical Center; Jacob.A.Buford@hitchcock.org.

Journal of Visualized Experiments : Jove
|June 2, 2025
PubMed
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This study optimized spatial transcriptomics for developmental research using zebrafish. The new method reduces costs by efficiently arranging multiple fish sections on a single slide for gene expression analysis.

Area of Science:

  • Biomedical Research
  • Developmental Biology
  • Genomics

Background:

  • Spatial transcriptomic techniques offer valuable insights into gene expression patterns within tissues.
  • High costs associated with imaging and analyzing multiple samples limit their application, especially in extensive developmental studies.
  • Developing cost-effective methods is crucial for advancing spatial transcriptomics in research.

Purpose of the Study:

  • To optimize spatial transcriptomic specimen arrangement for cost reduction in developmental studies.
  • To adapt and refine techniques for processing multiple zebrafish samples for in situ spatial transcriptomic analysis.
  • To enhance the efficiency and affordability of spatial transcriptomic studies using a vertebrate model.

Main Methods:

  • Utilized zebrafish (Danio rerio) as a developmental model due to transparency, genetic homology to humans, and small size.

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Last Updated: Sep 19, 2025

Spatially Compact Arrangement of Larval Zebrafish Sections for Spatial Transcriptomic Analysis
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Spatially Compact Arrangement of Larval Zebrafish Sections for Spatial Transcriptomic Analysis

Published on: May 16, 2025

476
Using an Automated 3D-tracking System to Record Individual and Shoals of Adult Zebrafish
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  • Developed optimized protocols for fixation, cryosectioning, and alignment of serial sections from multiple zebrafish.
  • Successfully processed up to 174 serial sections from multiple biological replicates within a standard 22 mm x 10.5 mm imaging area.

    • Main Results:

    • Achieved reliable alignment and high-quality sectioning of multiple zebrafish samples on a single slide.
    • Demonstrated the feasibility of processing numerous sections from zebrafish as young as 15 days post fertilization (dpf).
    • Significantly optimized throughput and reduced per-sample costs for spatial transcriptomic analysis.

    Conclusions:

    • The developed method effectively reduces the cost of spatial transcriptomic analysis in developmental studies.
    • Zebrafish are a suitable model for compact specimen arrangement, enabling simultaneous processing of multiple samples.
    • This optimization enhances the accessibility and scalability of spatial transcriptomic techniques for biological research.