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Updated: Jan 2, 2026

Isolation and Characterization of Single Cells from Zebrafish Embryos
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Published on: March 12, 2016

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A single-cell transcriptome atlas for zebrafish development.

Dylan R Farnsworth1, Lauren M Saunders2, Adam C Miller1

  • 1Institute of Neuroscience, University of Oregon, Eugene, OR, USA.

Developmental Biology
|November 30, 2019
PubMed
Summary
This summary is machine-generated.

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Researchers created a single-cell transcriptome atlas of developing zebrafish, identifying 220 cell clusters. This resource maps gene expression changes during organogenesis, advancing understanding of animal development and disease.

Area of Science:

  • Developmental Biology
  • Genomics
  • Zebrafish Model Organisms

Background:

  • Defining cell types and their developmental trajectories is crucial for understanding animal development and human diseases.
  • Current knowledge gaps exist in fully characterizing distinct cell types and the gene expression patterns driving their formation during development.

Purpose of the Study:

  • To create a comprehensive single-cell transcriptome atlas of developing zebrafish.
  • To investigate gene expression dynamics from the pharyngula to early larval stages.
  • To provide a resource for understanding cell-type specification and organogenesis.

Main Methods:

  • Single-cell RNA sequencing (scRNA-seq) was employed to profile gene expression.
  • Transcriptional profiles were generated from 44,102 cells across four days of zebrafish development.

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  • Experiments were duplicated to ensure high reproducibility.

    • Main Results:

    • A single-cell transcriptome atlas of developing zebrafish was successfully generated.
    • 220 distinct cell clusters were annotated, revealing cell type diversity.
    • Strategies for analyzing gene expression changes at single-cell resolution during development were highlighted.
    • New cell-type or developmental stage-specific expression information was assigned to numerous genes.

    Conclusions:

    • The zebrafish single-cell transcriptome atlas provides a valuable resource for biological research.
    • The atlas facilitates hypothesis generation for functional analysis of gene roles in development.
    • This work contributes to defining cell-type diversity and transcriptional profiles during zebrafish organogenesis.