Zebrahub: A single-cell atlas of zebrafish vertebrate development


Zebrahub is a multimodal, single-cell RNA sequencing atlas of vertebrate development at single-embryo resolution, using zebrafish as a model organism.

The first Zebrahub dataset, of approximately 120,000 cells spans 10 developmental stages: from end-of-gastrulation embryos to 10-day larvae (bud-stage, 5-, 10-, 15-, 20-, 30-somites stages, as well as 2-, 3-, 5- and 10-days post-fertilization). Four embryos were sequenced per time point.

We strive to achieve the highest possible quality; in that context, we expect the Zebrahub dataset to evolve to include more stages and higher data resolution.

The Royer Group leads this work in collaboration with CZ Biohub’s Data Science and Genomics Platforms. We aim to provide an easy-to-navigate dataset, with single-embryo consistent and high-quality resolved picture of development leveraging the latest single-cell technologies. Zebrahub adds one more species, Danio rerio, to CZ Biohub’s several single-cell atlases.

Zebrahub datasets have been key for our own upcoming and future work on deciphering vertebrate development, we hope that it will also prove useful for the zebrafish research community at large.