Single-cell reconstruction of developmental trajectories during zebrafish embryogenesis

Farrell JA* and Wang Y*, Riesenfeld SJ, Shekhar K, Regev A* and Schier AF*. Single-cell reconstruction of developmental trajectories during zebrafish embryogenesis. Science 26 April 2018. doi: 10.1126/science.aar3131


Contacts: Jeff Farrell (, Yiqun Wang (, and Alex Schier (


Overview of study: 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. This portal presents 38,731 single-cell transcriptomes generated using Drop-seq from 694 embryos across 12 closely spaced stages of early zebrafish development. Timepoints spanned from high blastula stage (3.3 hours post-fertilization, just after transcription from the zygotic genome begins), when most cells are pluripotent, to 6-somite stage (12 hours post-fertilization, shortly after the completion of gastrulation), when many cells have differentiated into specific cell types. 



URD Force-directed Layout Cell Type Label Abbreviations: Adax (Adaxial cells), CM (Cephalic Mesoderm), Di (Diencephalon), EndoPhar (Pharyngeal Endoderm), EndoPanInt (Pancreatic & Intestinal Endoderm), Epi (Epidermis), EVL (Enveloping Layer Cells / Periderm), HB R3 (Hindbrain Rhombomere 3), HB R4 (Hindbrain Rhombomere 4), HB R5-6 (Hindbrain Rhombomeres 5 & 6), Heart (Heart Primordium), HemICM (Hematopoietic Intermediate Cell Mass), HemRBI (Hematopoietic Rostral Blood Island), MB (Midbrain), NC (Neural Crest), Noto (Notochord), NPB (Neural Plate Border), Optic (Optic Cup), PCP (Prechordal Plate), PGC (Primordial Germ Cells), Padeno (Adenohypophyseal Placode), Pepi (Epibranchial Placode), Plens (Lens Placode), Polf (Olfactory Placode), Potic (Otic Placode), Ptrig (Trigeminal Placode), Pro (Pronephros Primordium), SC (Spinal Cord), Som (Somites), Tel (Telencephalon), TB (Tailbud).


How to use the Broad Single-cell Portal:



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Single-cell reconstruction of developmental trajectories during zebrafish embryogenesis
Science 2018 Jun 1;360(6392):eaar3131