GEO series

Single-cell reconstruction of developmental trajectories during zebrafish embryogenesis

GSE106587 Danio rerio Expression profiling by high throughput sequencing 446 samples Submitted 2018/04/27 Platform GPL20828Platform GPL18413

Summary

During embryogenesis, cells acquire distinct fates by transitioning through transcriptional states. To uncover these transcriptional trajectories during zebrafish embryogenesis, we sequenced 38,731 cells and developed URD, a simulated diffusion-based computational reconstruction method. URD identified the trajectories of 25 cell types through early somitogenesis, gene expression along them, and their spatial origin in the blastula. Analysis of Nodal signaling mutants revealed that their transcriptomes were canalized into a subset of wild-type transcriptional trajectories. Some wild-type developmental branchpoints contained cells expressing genes characteristic of multiple fates. These cells appeared to trans-specify from one fate to another. These findings reconstruct the transcriptional trajectories of a vertebrate embryo, highlight the concurrent canalization and plasticity of embryonic specification, and provide a framework to reconstruct complex developmental trees from single-cell transcriptomes. This SuperSeries is composed of the SubSeries listed below.

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Direct links to NCBI, no account and no request form: the whole study as GSE106587_RAW.tar, processed values as the series matrix, the supplementary file directory, and per-sample supplementary files for any of the 446 samples. Raw sequencing reads are also available from ENA.

Whole study · RAW.tar ↓ Series matrix ↓ All supplementary files ↗ Raw reads on ENA ↗

Also filed as BioProject PRJNA417291 and SRA study SRP123526. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 29700225) ↗

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