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Here, you'll find data and code to reproduce analyses in the papers or explore the data for yourself.

For code and processed tables, please visit our GitHub repository.

Zebrafish developmental reference atlas

Zebrafish developmental time series and tissue annotations.

Reference Atlas

A processed and annotated monocle3 cell_data_set object (.RDS file) containing ~1.25M cells of wild type zebrafish development. This reference includes both the uninjected controls (this dataset only) and the injected-control embryos (also in the perturbation atlas).

Reference atlas

For individual parts of the dataset:

Raw count matrix (.mtx) Cell metadata (.csv) Gene metadata (.csv)

Processed data subsets:

  • Subclustered and finely annotated sensory cranial ganglia cells (plus Rohon-Beard neurons). This dataset contains just wild type and control-injected cells.

Cranial ganglia subset (.RDS)

  • Subclustered and finely annotated notochord and parachordal cartilate cells (control-injected and wild type only).

Notochord subset (.RDS)

Zebrafish CG and Notochord

Subclustered cranial sensory ganglia and notochord cells over developmental time.
  • Subclustered hindbrain (HB) cells from Figure 3, with motor neurons (66k cells) and without (60k cells). The hindbrain-related genetic targets -- egr2b, cdx4, cdx4; cdx1a, epha4a, hoxb1a, mafba -- are included in addition to injected-controls. Timepoints included are 18, 24, and 36 hpf.

HB + motor neurons (.RDS) HB - motor neurons (.RDS)

Genetic Perturbation Atlas

A processed and annotated monocle3 cell_data_set object (.RDS file) containing 2M cells from control-injected and perturbed zebrafish embryos. Timepoints: 18, 24, 36, 48, 72 hpf.

Perturbation atlas

For individual parts of the dataset:

Raw count matrix (.mtx) Cell metadata (.csv) Gene metadata (.csv)

Temperature Atlas

A processed and annotated monocle3 cell_data_set object (.RDS file) containing 400,000 cells from embryos raised at increased temperature (28°C, 32°C, and 34°C).

Temperature atlas

For individual parts of the dataset:

Count matrix (.mtx) Cell metadata (.csv) Gene metadata (.csv)

Additional data files:

Background art by Elena Bansh.