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 Further acknowledgements goes to all the data producers (see DCC) particularly those, who submitted unpublished data: Elisabeth Busch-Nentwich (Sanger), Antonio Giraldez (Yale), Tatjana Sauka-Spengler (Oxford), Jose Louis Gomez Skarmeta (UPO Sevilla) and their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
The Chinese zebrafish research community has been rapidly growing in recent years. Since 2012, the Chinese Zebrafish Principal Investigator Meeting (CZPM) has been held in Wuhan by the China Zebrafish Resource Center (http://zfish.cn). The CZPM is a biennial meeting series for scientists who are interested in basic and applied science in zebrafish and other fish models.
The 4th CZPM will take place from October 11th to 14th, 2018. The organizers welcome all participants who wish to take this opportunity to exchange research results, to share ideas, and to promote collaborations.
For more information, please visit the meeting website: http://pi2018.zfish.cn/ .
Yonghua Sun, Institute of Hydrobiology, Chinese Academy of Sciences
Feng Liu, Institute of Zoology, Chinese Academy of Sciences
Zhan Yin, Institute of Hydrobiology, Chinese Academy of Sciences
Anming Meng, Tsinghua University
We are happy to inform you that registration for the Nordic Zebrafish and Husbandry meeting is now open. The deadline for registration is the 8th of October 2018. You are invited to submit abstracts for either the oral or poster presentation. The participation fee is 1000 SEK and includes all coffee breaks, lunches and the dinner/social event.
Registration: https://survey.ki.se/nordic_zebrafish
For more information, please visit the meeting website:
https://ki.se/en/km/nordic-zebrafish-and-husbandry-meeting-2018
We look forward to seeing you in Stockholm in November 2018!
Dear Colleagues,
For a workshop, sponsored by ORIP/NIH end of July, we are seeking community feedback to discuss and assess the needs and challenges of developing defined diets and optimized feed management strategies that will support normal zebrafish development and physiology and will facilitate the analysis of phenotypes in a standardized nutritional environment. This will promote rigor and reproducibility in some zebrafish studies and enhance the use of zebrafish and other aquatic models in biomedical research.
A more detailed description of workshop purpose and objectives is below. The organizers would very much appreciate your thoughts on the issue. Please provide your feedback through this survey:
Workshop Organizing Committee (WOC) members:
Diana Baumann (Stowers Institute for Medical Research, MO)
Lilianna Solnica-Krezel (Washington University School of Medicine, MO)
John Rawls (Duke University School of Medicine, NC)
Robert Tanguay (Oregon State University, OR)
Zoltan Varga (ZIRC, University of Oregon, Eugene, OR)
Stephen A. Watts (Chair; University of Alabama at Birmingham, AL)
Follow this link to the Survey:
Or copy and paste the URL below into your internet browser:
https://oregon.qualtrics.com/jfe/preview/SV_3gTZ0U77pWzqTVH?Q_CHL=preview
Follow the link to opt out of future emails:
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Workshop: Defined Diets for Zebrafish and Other Aquatic Biomedical Research Models: Needs and Challenges
ORIP/DPCPSI/OD-NIH sponsored Workshop
Purpose of the Meeting: Aquatic animal species, such as zebrafish (Danio rerio), are powerful models for studying human development, behavior, genetics, and disease. The ability to produce transgenic and mutant lines provides biomedical researchers with many options for developing models of human diseases and for developing relevant therapeutic approaches. Different facilities and laboratories use a variety of diets and feeding protocols to maintain these models. In many laboratories zebrafish are reared with a combination of live feed (ex vivo) and/or one of many undefined commercial diets. Commercial diets used in zebrafish husbandry differ significantly in ingredient and nutrient composition and often contain preservatives, lakes, dyes, antinutritional factors, or bioactive food compounds. Studies indicate that the length, weight, sexual maturation, fecundity, and mortality of zebrafish can vary significantly with different diets. Unfortunately, impacts of diet on zebrafish health and behavior and corresponding implications for zebrafish research outcomes are not well described. Currently, the daily dietary nutrient requirements of almost all nutrients have not been investigated. There is also no consensus among aquatic facilities, researchers, and commercial vendors on nutritional requirements at various life stages (i.e., larval, juvenile, and adult) or for particular research applications to minimize husbandry variations among aquatic facilities or laboratories. Complicit in this lack of consensus is a community-wide lack of understanding of the role of nutrition in animal development, health, and research outcomes. To address this gap, the Office of Research Infrastructure Programs (ORIP) is sponsoring a workshop to bring together members of the zebrafish scientific community, with expertise in zebrafish and other aquatic and relevant models, for a day of discussion. The workshop attendees will assess the needs and challenges of developing defined diets and optimized feed management strategies that will support normal zebrafish development and physiology and will facilitate the analysis of phenotypes in a standardized nutritional environment. Standardization and education will promote rigor and reproducibility in some zebrafish studies and enhance the use of zebrafish and other aquatic models in biomedical research.
Objectives:
- Review diet development strategies, where available, in other biomedical model species.
- Assess the current nutrition status of zebrafish.
- Describe the need for defined diets for maintenance and experimental stocks, including assessment of life stage requirements.
- Discuss the potential impact of defined diets on genetic stocks used in biomedical research, their effect on development, physiology and expressivity of disease/mutant phenotypes.
- Identify obstacles and evaluate strategies that may lead to a successful consensus, acceptance, and implementation of defined diets among the different scientific community stakeholders.
- Define an educational approach to informing the community and associated partners (journals, organizations, granting agencies, etc.)
- Determine whether/how the approach to develop a defined diet for zebrafish could be applied to other aquatic models, and animal models in general.