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Updated: May 2, 2026

Quantitative Analysis of Protein Expression to Study Lineage Specification in Mouse Preimplantation Embryos

Quantitative Analysis of Protein Expression to Study Lineage Specification in Mouse Preimplantation Embryos

Published on: February 22, 2016

Embryo-scale reverse genetics at single-cell resolution.

Lauren M Saunders¹, Sanjay R Srivatsan¹, Madeleine Duran¹

¹Department of Genome Sciences, University of Washington, Seattle, WA, USA.

|November 15, 2023

Summary

This summary is machine-generated.

This study presents a comprehensive zebrafish atlas of perturbed embryos, revealing cell type variations and genetic dependencies during development. The data enables new hypotheses on skull development and addresses challenges in developmental genetics.

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Area of Science:

Developmental Biology
Genomics
Cell Biology

Background:

Single-cell transcriptomic technologies have advanced cellular atlas generation from whole embryos.
Existing atlases often lack data on developmental variation across individual embryos.
Understanding latent variation is crucial for a complete picture of development.

Purpose of the Study:

To create a comprehensive single-cell transcriptomic atlas of perturbed zebrafish embryos.
To analyze developmental variation and genetic dependencies across a large number of individual embryos.
To identify novel cell populations and developmental trajectories influenced by genetic perturbations.

Main Methods:

Generated single-cell transcriptomic data from 1,812 individually resolved zebrafish embryos.
Covered 19 timepoints and 23 genetic perturbations, totaling 3.2 million cells.
Employed high replication (≥8 embryos/condition) to estimate variance and detect deviations.

Main Results:

Detected perturbation-dependent cell type composition changes relative to wild-type embryos.
Resolved developmental trajectories and genetic dependencies in rare cranial ganglia neurons (<1% of embryo).
Identified brachyury-independent cells with notochord sheath cell transcriptomes, suggesting new skull development origins.

Conclusions:

Standardized, high-resolution, organism-scale single-cell data is key for mapping genetic dependencies in zebrafish.
This atlas addresses developmental genetics challenges, including cellular and transcriptional plasticity.
The findings provide new hypotheses for early skull development and individual phenotypic diversity.