The DANIO-CODE consortium has generated a comprehensive compendium of published and unpublished genomic, epigenomic and transcriptomic datasets from zebrafish. The resource in its current version Freeze02 covers 38 stages of wild-type embryonic zebrafish development from fertilisation to free feeding larva as well as tissues of adult forms and comprises nearly 1000 sequencing samples of 17 assay types.
The sample descriptions (annotations), the re-analyses of the sequencing data by standardised computational pipelines and the derived annotations, such as the atlas of regulatory elements, are free to search, download and use. The consortium's main publication appeared in Nature Genetics in 2022, so the pre-publication restrictions that applied to earlier releases no longer apply.
If you use DANIO-CODE data or annotations in your work, please cite:
Baranasic D, Hörtenhuber M, Balwierz PJ, et al. Multiomic atlas with functional stratification and developmental dynamics of zebrafish cis-regulatory elements. Nature Genetics 54, 1037–1050 (2022). https://doi.org/10.1038/s41588-022-01089-w
Much of the raw data was originally generated by other laboratories. Please also cite the original publications of the datasets you use; where known, they are listed on each series page in the DCC.
To refer to the DCC platform itself, please cite: Hörtenhuber M, et al. *-DCC: a platform to collect, annotate, and explore a large variety of sequencing experiments. GigaScience 9, giaa024 (2020). https://doi.org/10.1093/gigascience/giaa024
You can acknowledge the data source with: "Zebrafish data were obtained from the DANIO-CODE Data Coordination Centre (https://danio-code.irb.hr)."
For technical enquiries contact daniocode@gmail.com; for DANIO-CODE publication policies and other enquiries contact daniocode.enquiries@gmail.com.