Single-cell analysis of shared signatures and transcriptional diversity during zebrafish development

Published: 16 November 2023| Version 1 | DOI: 10.17632/3378fwwm8j.1


During development, animals generate distinct cell populations with specific identities, functions, and morphologies. We mapped transcriptionally distinct populations across 489,686 cells from 62 stages during wild-type zebrafish embryogenesis and early larval development (3–120 hours post-fertilization). Using these data, we identified the limited catalog of gene expression programs reused across multiple tissues and their cell-type-specific adaptations. We also determined the duration each transcriptional state is present during development and suggest new long-term cycling populations. Focused clustering and transcriptional trajectory analyses of non-skeletal muscle and endoderm identified transcriptional profiles and candidate transcriptional regulators of understudied cell types and subpopulations, including the pneumatic duct, individual intestinal smooth muscle layers, spatially distinct pericyte subpopulations, and recently discovered best4+ cells. To enable additional discoveries, we make this comprehensive transcriptional atlas of early zebrafish development available through our website, Daniocell. This repository contains unprocessed acquisitions of microscopy presented in the study.



National Institute of Child Health and Human Development Division of Intramural Research


Developmental Biology, Danio Rerio, Smooth Muscle, Intestine, Pericyte


Eunice Kennedy Shriver National Institute of Child Health and Human Development

1 ZIA HD 008997