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Updated: Oct 29, 2025

Isolation and Characterization of Single Cells from Zebrafish Embryos

Isolation and Characterization of Single Cells from Zebrafish Embryos

Published on: March 12, 2016

Single-cell transcriptome analysis of the zebrafish embryonic trunk.

Sanjeeva Metikala^1,2, Satish Casie Chetty^1,3, Saulius Sumanas^1,2,4

¹Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States of America.

|July 8, 2021

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Researchers mapped the transcriptional signatures of 27 cell types in zebrafish embryos using single-cell RNA sequencing. This developmental biology resource aids understanding of cell lineage choices.

Area of Science:

Developmental Biology
Cellular Biology
Genomics

Background:

Cell differentiation during embryonic development creates diverse cell types with unique transcriptional profiles.
Characterizing these transcriptomic signatures is crucial for understanding developmental processes.
Previous studies have only partially mapped the transcriptional landscape of developing cell lineages.

Purpose of the Study:

To comprehensively identify and annotate the transcriptional signatures of various cell types and subtypes during zebrafish embryonic development.
To create a detailed transcriptomic dataset of over 20,000 cells from zebrafish embryos.
To provide a resource for studying the molecular mechanisms governing cell lineage decisions.

Main Methods:

Single-cell RNA sequencing (scRNA-seq) was employed to analyze individual cells.

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Sample Preparation and Analysis of RNASeq-based Gene Expression Data from Zebrafish

Published on: October 27, 2017

Related Experiment Videos

Last Updated: Oct 29, 2025

Isolation and Characterization of Single Cells from Zebrafish Embryos

Isolation and Characterization of Single Cells from Zebrafish Embryos

Published on: March 12, 2016

Large-scale Zebrafish Embryonic Heart Dissection for Transcriptional Analysis

Large-scale Zebrafish Embryonic Heart Dissection for Transcriptional Analysis

Published on: January 12, 2015

Sample Preparation and Analysis of RNASeq-based Gene Expression Data from Zebrafish

Sample Preparation and Analysis of RNASeq-based Gene Expression Data from Zebrafish

Published on: October 27, 2017

Transcriptomic analysis was performed on over 20,000 cells disaggregated from the trunk region of zebrafish embryos.

Cells were analyzed at the 30 hours post-fertilization (hpf) developmental stage.

Main Results:

Transcriptional signatures for 27 distinct cell types and subtypes were identified and annotated.
The study generated a high-resolution transcriptomic map of zebrafish embryonic trunk cells.
The data revealed the molecular diversity underlying cell differentiation.

Conclusions:

The identified transcriptomic signatures provide a valuable resource for researchers in developmental and cellular biology.
This dataset facilitates a deeper understanding of the molecular mechanisms controlling cell lineage choices.
The findings contribute to the broader knowledge of embryonic development and cell fate determination.