10 stages, 40 embryos, ~120000 cells, more to come...

Single-Embryo Single-Cell RNA Sequencing Atlas

of Zebrafish Development

Zebrahub's inaugural release of a single-cell RNA sequencing timecourse dataset, which offers a detailed account of zebrafish development at the resolution of individual embryos. This comprehensive dataset encompasses 10 developmental stages, ranging from end-of-gastrulation embryos to 10-day-old larvae (including bud-stage, 5-, 10-, 15-, 20-, 30-somite stages, as well as 2-, 3-, 5-, and 10-days post-fertilization), with four embryos sequenced per time point and a total of around 120,440 cells analyzed. Our goal is to provide a user-friendly and high-quality single-embryo resolved timecourse dataset that leverages the latest single-cell technologies, providing a comprehensive view of development.

More details about the experimental protocol can be found here.

Full Dataset

Full zebrahub single cell dataset, rotating 3D umap,

Full Dataset

10 stages, 40 embryos



zebrafish embryo,  10 hpf, bud stage

10 hpf

Bud stage

zebrafish embryo,  12 hpf, 5 somites

12 hpf

5 somites

zebrafish embryo,  14 hpf, 10 somites

14 hpf

10 somites

zebrafish embryo,  16 hpf, 15 somites

16 hpf

15 somites

zebrafish embryo,  19 hpf, 20 somites

19 hpf

20 somites

zebrafish embryo,  1 dpf, 30 somites

1 dpf

30 somites

zebrafish embryo,  2 dpf, Larva

2 dpf


zebrafish embryo,  3 dpf, Larva

3 dpf


zebrafish embryo,  5 dpf, Larva

5 dpf


zebrafish embryo,  10 dpf, Larva

10 dpf



hpf = hours post fertilization
dpf = days post fertilization

Cluster Annotation

We generated UMAPs for each developmental stage by combining the data of all individually sequenced embryos (four embryo replicates per stage). Per time point, we computed Leiden clusters, which we annotated based on the expression of specific enriched genes followed by a literature search and ZFIN database queries, as well as existing published and annotated scRNAseq data (Farrell et al. 2018; Wagner et al. 2018; Farnsworth et al. 2020; Raj et al. 2020).

For the global UMAP we integrated all the developmental stages together to get a temporally coherent cell-type annotation. Annotations were done using information from previously annotated single UMAPs, cross-validated with a literature search based on enriched genes per cluster groups. We leveraged the Zebrafish Anatomy Ontology (ZFA) to provide the community with cell-type annotations that use the controlled vocabulary provided by the ZFA.

Notes on Annotation

Zebrahub is an ongoing project and we are working on improving the resolution of our annotations over time. We welcome collaboration to improve the quality of the cell-type annotations and/or other metadata variables. Therefore if you detect any ambiguity in the current data objects or want to help us on a specific region or cluster please contact us.