DANIO-CODE: First release of track hub

Dear zebrafish user community, 

we are proud to announce the first release of the DANIO-CODE track hub for zebrafish developmental epigenomics and transcriptomics datasets. It contains almost a 1000 tracks with 17 assay types (ChIP-seq, RNA-seq, ATC-seq, CAGE-seq etc.) from 38 stages of development. The raw data of 30 labs were annotated and reanalyzed by standardised pipelines to create the track hub, which is currently available to upload to UCSC or Ensembl genome browsers at https://danio-code.zfin.org. 

For information on how to access data, on fair use policy and how to upload new data to the resource, please visit the Data Coordination Centre: https://danio-code.zfin.org.

To learn more about DANIO-CODE visit https://www.birmingham.ac.uk/generic/danio-code/index.aspx.

For enquiries on technical matters contact daniocode@gmail.com.

For general enquiries contact daniocode.enquiries@gmail.com. 

Please spare some time to browse the datasets and to check you favourite gene, to reveal its expression and its true promoter, to predict its enhancers and non-coding RNAs around them and many more…The first release is a beta version, please send feedback to the emails above.

Acknowledgements:

Massive thank you to Matthias Hörtenhuber, Kadir Mukarram, Michael Dong and Carsten Daub at Karolinska Institutet as well as to Damir Baranasic and Boris Lenhard at Imperial College, who have been the main drivers behind the recently achieved DANIO-CODE milestone. 

Thanks extend to Marcus Stoiber at Berkeley and Ben Brown at Berkeley/Birmingham for their work at the early stages of data collecting/processing pipeline development. Anne Eagle, Monte Westerfield and their colleagues at ZFIN for hosting and managing the datasets and WIKI, Matthias Hörtenhuber, Julia Horsefield (Otago), Bernard Peers (Liege) and Shelley Jukes (Birmingham) for helping with management and Fiona Wardle (KCL), Boris Lenhard for their major contributions in lobbying/applying for funds and DANIO-CODE meeting organisations. Further acknowledgements goes to all the data producers (see DCC) particularly those, who submitted unpublished data: Elisabeth Busch-Nentwich (Sanger), Antonio Giraldez (Yale), Tatjana Sauka-Spengler (Oxford), Jose Louis Gomez Skarmeta (UPO Sevilla) and their colleagues. Finally, we need to acknowledge the financial support by the European Commission’s  H2020 Marie Sklodowska-Curie programme to ZENCODE-ITN and the BBSCR, UK. 

We hope this achievement will not only help in learning about the zebrafish genome, it will also motivate all of us to submit additional, published and unpublished datasets to keep this resource growing for the benefit of the user community. 

Again, huge thanks to those who did this great job and wishing you as much fun as we have had with browsing the datasets in their full glory:).  

best wishes, 

Ferenc

On behalf of DANIO-CODE and ZENCODE-ITN partners

Ferenc Mueller f.mueller@bham.ac.uk