Zebrafish Links
Zebrafish International Resource Center (ZIRC)
ZIRC, housed on the University of Oregon campus in Eugene, provides a central repository for wild-type and mutant strains of zebrafish (Danio rerio) and for materials and information about zebrafish research. ZIRC commercially provides fish stocks, frozen sperm, antibodies, gene probes, and other markers to analyze wild-type and mutant stocks. They also offer pathological services and provide information for maintaining proper zebrafish health.
ZIRC and ZFIN are sister organizations. ZIRC resources and services are extensively cross-linked to ZFIN.
Zebrafish Information Network (ZFIN)
ZFIN is an integrated database for querying and displaying information for facilitating the use of the zebrafish
(Danio rerio) as animal model of human biology.
The site contains a section devoted to biological resources: anatomical information, laboratory protocols, antibodies, gene expression markers, gene nomenclature, zebrafish line information, etc.
ZFIN also serves as a hub of community news and announcements as well as being a central repository for contact information to other individuals, laboratories and companies involved with zebrafish applications.
Tübingen Zebrafish Stockcenter:
The Max-Planck Institute
The stockcenter keeps about 400 mutant zebrafish lines, which are publicly available for scientific research. Most of the mutants in the stockcenter were isolated in a screen for embryonic visible phenotypes in Tübingen between 1992-1994. In addition to mutants with embryonic visible phenotypes several dominant and recessive adult visible mutants are being kept (Haffter et al., 1996a; Haffter et al., 1996b).
From the 1,200 mutations that were analysed, the stockcenter keeps a subset as outbred lines of carrier fish. The mutant stocks include alleles of some of the 371 genes described (Tü ZF genes), as well as a number of wildtype and reference strains with visible markers. Most mutants that are not sufficiently characterized and not assigned to complementation groups (“unresolved”) are only kept as frozen sperm samples. As a rule these alleles will not be made available.
The collection of mutants kept as live fish in the stockcenter is in some flux. Because of limited capacity, we will remove a portion of the current strains, particularly those which have not met with any interest from researches until now. Other strains carrying newly induced mutations may be added instead. The stockcenter will normally provide outcrosses of mutant strains.
Zebrafish Husbandry Association (ZHA)
ZHA is a professional organization dedicated to promoting the improvement of husbandry standards for usage of the zebrafish (Danio rerio) in scientific research. ZHA seeks to: gather, review, and disseminate scientific information related to zebrafish biology and culture; develop new and improved husbandry standards based upon published scientific information and ongoing research; facilitate the exchange of zebrafish husbandry-related information; design and execute collaborative research projects in various areas of zebrafish culture and biology with the expressed intent of eventual publication in peer-reviewed scientific journals; and professionalize the field of zebrafish husbandry, especially for those working in biomedical research aquaculture facilities (managers, technicians, etc.).
ZF-MODELS
Zebrafish Models for Human Development and Disease is an integrated project funded by the European Commission. The aim of this project is to exploit the advantages of the zebrafish as a model organism for vertebrate development and human disease. A total of 29 groups at 15 different institutions in France, Germany, Italy, the Netherlands, Norway, Switzerland and the United Kingdom are working together to produce new insights into how genes control development and ageing in vertebrates, using the zebrafish as a model organism.
Vertebrate Genome Annotation Database (Vega)
First made public in 2004, Vega has been designed to view manual annotation of human, mouse and zebrafish genomic sequences produced at the Wellcome Trust Sanger Institute. Since its initial release, the number of human annotated loci has more than doubled to close to 33 000 and now contains comprehensive annotation on 20 of the 24 human chromosomes, four whole mouse chromosomes and around 40% of the zebrafish Danio rerio genome.
FishMap
FishMap is a unified and centralized resource for storage, retrieval, and display of genomic information of the zebrafish. The datasets have been methodically collected from various resources and supplementary information of publications and mapped to the zebrafish genome. The data are organized into nine major sections, which include comparative genomics, mapping and sequencing, gene and gene predictions, expression and regulation, and variation and repeats. A number of unique sections have been incorporated, which include tracks on noncoding gene annotation, location of retrovirus/transposon integrations in the genome, and their flanking genomic sequences and novel transcripts. The datasets are linked to related data sources. The resource also features a Web-based BLAST server for sequence homology search and a gene ID converter that would enable users to sift through different interchangeable gene annotation identifier systems.
Sanger Institute: Danio rerio Project
In February 2001 the Sanger Institute started sequencing the genome of the zebrafish (Danio rerio). To obtain the genome sequence the institute maps and sequences clones from BAC libraries. The finished clones are manually annotated and accessible in Vega. To provide additional data whilst the above project is ongoing, the institute also generates integrated whole genome assemblies by filling in the yet existent gaps between clone contigs with whole genome shotgun sequence. These assemblies are then automatically annotated and accessible in Ensembl.
Zebrafish GenomeWiki
The Zebrafish GenomeWiki is a shared genomics resource for community annotation of the zebrafish genome. Members of the zebrafish community can annotate, comment and edit existing data sets using the Zebrafish GenomeWiki portal. The Zebrafish GenomeWiki will permit community experts and individual investigators to add the latest genomics information and discuss alternative annotations there by speeding up the fine annotation the zebrafish genome.
Ensembl!
The Ensembl project was started in 1999, some years before the draft human genome was completed. Even at that early stage it was clear that manual annotation of 3 billion base pairs of sequence would not be able to offer researchers timely access to the latest data. The goal of Ensembl was therefore to automatically annotate the genome, integrate this annotation with other available biological data and make all this publicly available via the web. Since the website's launch in July 2000, many more genomes have been added to Ensembl and the range of available data has also expanded to include comparative genomics, variation and regulatory data. The Ensembl project is headed by Paul Flicek and Steve Searle, and receives input from an independent scientific advisory board.
Google Bionet
Bionet is an online bulletin board system and is intended primarily to be a forum for individuals
interested in the scientific research of Danio rerio, commonly known as the zebrafish or zebra danio. The establishment of
this newgroup is in part a response to a request by attendies at a Cold Spring Harbor Symposium in April of 1993 for increased Internet interaction. The newsgroup is unmoderated; members are welcome to use it any way you they like: for asking questions; asking for assistance or for specific reagents (libraries, clones, antibodies, etc.); posting information regarding job opportunities; posting information regarding events; or in any other manner that seems appropriate.
Collaborators
Leonard I. Zon Laboratory:
Children's Hospital of Boston and Howard Hughes Medical Institute
Harold von Boehmer Laboratory:
Dana-Farber Cancer Institute and Harvard Medical School
David Langenau Laboratory:
Massachusetts General Hospital
Other Resources
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