PROJECT ID: GSE106587

Data source GEO: GSE106587
Description 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.
Key word endoderm formation; expression; fate; gene; gastrulation; fibroblasts; myoblasts; dynamics; casanova; protein
Publication Farrell JA, Wang Y, Riesenfeld SJ, Shekhar K et al. Single-cell reconstruction of developmental trajectories during zebrafish embryogenesis. Science 2018 Jun 1;360(6392). PMID: 29700225
Abstract 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 branch points contained cells that express 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 with which to reconstruct complex developmental trees from single-cell transcriptomes.


Dataset Information

Dataset ID Species Tissue / Organ Experiment type Sample Source dataset ID
1. GSE106587 (WT) Danio rerio embryo baseline 12hpf, 6 somites, wild-type TLAB embryo GEO: GSM3084402
2. GSE106587 (MZoep mutant) Danio rerio embryo baseline 12hpf, 6 somites, maternal zygotic oep tz57 mutant embryo GEO: GSM3084403

Clustering Result

Cluster Cell type Gene id (symbol) Marker class Evidence
3 Somites ENSDARG00000017917 (her7) marker DOI:10.1126/science.aar3131
4 Epidermal cells ENSDARG00000054616 (cldni) marker DOI:10.1126/science.aar3131
5 Optic cup ENSDARG00000052893 (rx3) marker DOI:10.1126/science.aar3131
5 Optic cup ENSDARG00000040321 (rx2) marker DOI:10.1126/science.aar3131
6 Heart primordium ENSDARG00000017821 (gata5) marker DOI:10.1126/science.aar3131
6 Heart primordium ENSDARG00000008305 (hand2) marker DOI:10.1126/science.aar3131
9 Mesoderm ENSDARG00000056913 (pcolcea) marker DOI:10.1126/science.aar3131
9 Mesoderm ENSDARG00000033971 (prrx1a) marker DOI:10.1126/science.aar3131
9 Mesoderm ENSDARG00000017195 (foxf2a) marker DOI:10.1126/science.aar3131
10 Endoderm ENSDARG00000104495 (pltp) marker DOI:10.1126/science.aar3131
10 Endoderm ENSDARG00000003411 (foxa2) marker DOI:10.1126/science.aar3131
12 Neural crest ENSDARG00000021032 (foxd3) marker DOI:10.1126/science.aar3131
12 Neural crest ENSDARG00000043923 (sox9b) marker DOI:10.1126/science.aar3131
12 Neural crest ENSDARG00000077467 (sox10) marker DOI:10.1126/science.aar3131
13 Neural crest ENSDARG00000021032 (foxd3) marker DOI:10.1126/science.aar3131
13 Neural crest ENSDARG00000043923 (sox9b) marker DOI:10.1126/science.aar3131
13 Neural crest ENSDARG00000077467 (sox10) marker DOI:10.1126/science.aar3131
14 Adaxial cells ENSDARG00000009438 (myog) marker DOI:10.1126/science.aar3131
15 Placode ENSDARG00000062892 (foxe3) marker DOI:10.1126/science.aar3131
16 Optic cup ENSDARG00000052893 (rx3) marker DOI:10.1126/science.aar3131
17 Floor plate ENSDARG00000068567 (shha) marker DOI:10.1126/science.aar3131
18 Hematopoietic cells ENSDARG00000013477 (gata1a) marker DOI:10.1126/science.aar3131
18 Hematopoietic cells ENSDARG00000019930 (tal1) marker DOI:10.1126/science.aar3131

Cluster Cell type Gene id (symbol) Marker class Evidence
2 Telencephalon ENSDARG00000070769 (foxg1a) marker DOI:10.1126/science.aar3131
3 EVL, Periderm ENSDARG00000017624 (krt4) marker DOI:10.1126/science.aar3131
4 Optic cup ENSDARG00000052893 (rx3) marker DOI:10.1126/science.aar3131
5 Placode Trigeminal ENSDARG00000101831 (irx1a) marker DOI:10.1126/science.aar3131
6 Tailbud -- (ta) marker DOI:10.1126/science.aar3131
6 Tailbud ENSDARG00000003399 (fgf8a) marker DOI:10.1126/science.aar3131
7 Optic cup ENSDARG00000052893 (rx3) marker DOI:10.1126/science.aar3131
8 Epidermal cells ENSDARG00000045887 (mmp30) marker DOI:10.1126/science.aar3131
9 Placode ENSDARG00000071560 (dlx4b) marker DOI:10.1126/science.aar3131
11 Neural crest ENSDARG00000021032 (foxd3) marker DOI:10.1126/science.aar3131
11 Neural crest ENSDARG00000043923 (sox9b) marker DOI:10.1126/science.aar3131
11 Neural crest ENSDARG00000077467 (sox10) marker DOI:10.1126/science.aar3131