Table 2.
Examples of zebrafish databases and societies
| Name | Content | Website |
|---|---|---|
| General databases | ||
| • ZFIN | Aggregation of known publications, mutants, morpholinos and antibodies for a given gene | https://zfin.org/ |
| • ZIRC | Mutants available in their inventory for a given gene | http://zebrafish.org/ |
| The zebrafish book | https://zfin.org/zf_info/zfbook/zfbk.html | |
| • LAZEN | Latin American zebrafish resource center | http://lazen.fcien.edu.uy/ |
| • EZRC | Europe’s international zebrafish resource center | https://www.ezrc.kit.edu/ |
| • CZRC | China’s national zebrafish resource center | http://en.zfish.cn/ |
| • TZCAS | Taiwan’s national zebrafish resource center | http://icob.sinica.edu.tw/tzcas/fishlines_zeth.html |
| • Norwegian zebrafish platform | Norway’s national consortium | http://zebrafish.no/#myAnchor |
| • Zebrafish–National BioResource Project | Japan’s organization that collects and distributes zebrafish lines | https://nbrp.jp/report/reportProject.jsp?project=zebrafish |
| • ZeBase | Database for zebrafish inventory and streamline facility operations and organization | https://zebase.bio.purdue.edu/ |
| Genomic databases | ||
| • Ensembl | Ensemble zebrafish genome assembly | https://useast.ensembl.org/Danio_rerio/Info/Index |
| • BLAST | Zebrafish sequence analysis and searchable reference sequence | https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastSearch&BLAST_SPEC=OGP__7955__9557 |
| • zfishbook | Gene break transposon mediated mutants available | http://www.zfishbook.org/ |
| • Genome browser gateway | Mapping genes within the zebrafish genome and between other sequenced species | http://genome.ucsc.edu/cgi-bin/hgGateway?hgsid=85282730&clade=vertebrate&org=Zebrafish&db=0 |
| • Genomic resources for zebrafish ZInC | A Wikipedia page specifically for zebrafish genomic databases | https://wiki.zfin.org/display/general/Genomic+Resources+for+Zebrafish |
| Insertional mutants in the zebrafish | https://research.nhgri.nih.gov/ZInC/ | |
| • ztrap | Expression patterns images of gene and enhancer trap lines | https://ztrap.nig.ac.jp/ztrap/ |
| • M6A-Atlas | A database for many animals, including zebrafish, of the N6-methyladenosine epitranscriptome | http://180.208.58.19/m6A-Atlas/ |
| • ZenoFishDb | A curated database of the xenograft studies performed in the zebrafish | https://konulab.shinyapps.io/zenofishdb/ |
| Zebrafish single cell databases | ||
| • Zebrahub | Zebrafish embryonic development that combines single cell RNA sequencing with live light-sheet imaging | https://zebrahub.ds.czbiohub.org/ |
| • Daniocell | Single cell expression data of the TL/AB zebrafish throughout development | https://daniocell.nichd.nih.gov/ |
| • ZSCAPE | Single cell RNA-sequencing comparing WT, genetic mutants and temperature perturbations | https://cole-trapnell-lab.github.io/zscape/ |
| Anatomy or Atlas databases | ||
| • Bio-Atlas | Zebrafish Anatomy with histological slides during development starting at 48 hpf through 12 months old | http://bio-atlas.psu.edu/zf/index.php |
| • ZFAP | The zebrafish anatomy portal contains annotated and 3D anatomy throughout development | http://www.rdvd.fr/ |
| • Vascular Anatomy atlas | Zebrafish vascular anatomy throughout development, both 2D and 3D images. | https://zfish.nichd.nih.gov/Intro%20Page/intro1.html |
| • Z Brain Atlas | Zebrafish neuroanatomy reference at 6 dpf with regional definitions | https://engertlab.fas.harvard.edu/Z-Brain/home/ |
| • mapzebrain | Zebrafish brain regions, neural connections and transgenic lines | https://fishatlas.neuro.mpg.de/ |
| • Brain Browser | Transgene patterns at 6 dpf | http://vis.arc.vt.edu/projects/zbb/ |
| • Zebrafishbrain | A high-resolution atlas of the developing zebrafish brain | https://zebrafishucl.org/zebrafishbrain#about-1 |
| • AZBA | A 3D atlas of the adult zebrafish brain | https://azba.wayne.edu/ |
| • FishFace | A database within FaceBase with zebrafish craniofacial development | https://www.facebase.org/resources/zebrafish/fishface/home/ |
| Zebrafish societies | ||
| • International Zebrafish Society | Fosters the collaboration within the international zebrafish community | https://www.izfs.org/ |
| • European Zebrafish Society | Central contact point for the European zebrafish community | https://www.ezsociety.org/ |
| • Polish Zebrafish Society | Zebrafish research society in Poland | https://zebrafish.org.pl/ |
| • Nordic Zebrafish Network | Bring together zebrafish enthusiasts to improve quality of husbandry and science | https://ki.se/en/research/research-infrastructure-and-environments/core-facilities-for-research/zebrafish-core-facility/the-nordic-zebrafish-network |
| • Zebrafish Disease Society | Focuses on the use of zebrafish in clinical research | https://www.zdmsociety.org/home |
| • Zebrafish Foundation India | The society works towards creating a strong zebrafish research community | https://zebfin.res.in/ |
| • InSDB | Zebrafish meetings and interactions in and around India are coordinated through the developmental biology society. | https://insdb.in/about-insdb/about-mission/ |
Due to the dynamic and expanding nature of the field, this table is an initial but incomplete list of the types of online databases and societies available to the zebrafish community. Many zebrafish societies are available regionally and in the area’s native language.