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Protocols

ZFIN specifications

Information


Unique identifier OMICS_01666
Name ZFIN
Alternative name The Zebrafish Information Network
Restrictions to use None
Community driven No
Data access Browse
User data submission Allowed
Maintained Yes

Taxon


  • Vertebrates
    • Danio rerio

Maintainer


  • person_outline Douglas G. Howe

Publications for The Zebrafish Information Network

ZFIN citations

 (95)
library_books

Transcriptomic Profiling of Zebrafish Hair Cells Using RiboTag

2018
PMCID: 5939014
PMID: 29765956
DOI: 10.3389/fcell.2018.00047

[…] ebrafish Expression Ontology of Gene Sets (ZEOGS) tool (Prykhozhij et al., ). This online tool can be used to detect overrepresented anatomical structures based on known gene expression patterns from the Zebrafish Information Network (ZFIN) (Howe et al., ). When analyzing the enriched gene set, the top result for overrepresented anatomy is “neuromast,” and also includes the inner ear HC types “hai […]

library_books

NCX DB: a unified resource for integrative analysis of the sodium calcium exchanger super family

2018
BMC Neurosci
PMCID: 5898058
PMID: 29649983
DOI: 10.1186/s12868-018-0423-2

[…] animal model organism databases that comprise the Alliance of Genome Resources (http://www.alliancegenome.org/). These are: WormBase (ver. WS260) [], XenBase (ver. 4.5.0) [], FlyBase (FB2017_04) [], the Zebrafish Information Network (ZFIN: https://zfin.org/), Mouse Genomics Informatics (http://www.informatics.jax.org/), and the Rat Genome Database (https://rgd.mcw.edu/). By including the Alliance […]

library_books

A comparative genomics study of carbohydrate/glucose metabolic genes: from fish to mammals

2018
BMC Genomics
PMCID: 5896114
PMID: 29642853
DOI: 10.1186/s12864-018-4647-4

[…] hodb.org/) and assessed orthology based on RBH (reciprocally best hit, performing an NCBI BLASTP search using the default parameters). We also manually verified each genome-specific gene according to ZFIN (Zebrafish International Resource Center database, http://zfin.org/), MGI (Mouse Genome Informatics, http://www.informatics.jax.org/), Xenbase (Xenopus model organism database, http://www.xenbase […]

library_books

An optimised pipeline for parallel image based quantification of gene expression and genotyping after in situ hybridisation

2018
PMCID: 5936060
PMID: 29535102
DOI: 10.1242/bio.031096

[…] to detect spatial expression patterns and tissue-specific changes in mRNA levels. Relevant protocols with several extensions have been standardised () and numerous validated probes are curated on the ZFIN database (). Using ISH to analyse MO phenotypes requires processing of the MO-treated and control samples separately, which may result in an inherent bias and an increased risk of technical varia […]

library_books

A Whole Brain Staining, Embedding, and Clearing Pipeline for Adult Zebrafish to Visualize Cell Proliferation and Morphology in 3 Dimensions

2018
Front Neurosci
PMCID: 5776138
PMID: 29386991
DOI: 10.3389/fnins.2017.00750

[…] tocol for the first time, only 1–2 brain samples are embedding at a time in low melting agarose (Figure ). Agarose embedding has long been used in zebrafish research for histology of fixed specimens (ZFIN; Tsao-Wu et al., ; Copper et al., ) or live in vivo confocal imaging of larvae (Kaufmann et al., ), and is commonly used during sample preparation for OPT scanning across leading animals models, […]

library_books

The endocannabinoid gene faah2a modulates stress associated behavior in zebrafish

2018
PLoS One
PMCID: 5756047
PMID: 29304078
DOI: 10.1371/journal.pone.0190897

[…] ntually establish populations of heterozygous F2 mutants []. The indels were characterized by sequencing, and the sperm from the F2 populations was cryopreserved []. The cnr1 mutant line was assigned the Zebrafish Information Network (ZFIN) designator cnr1mn49, and the faah2a mutant line was assigned the ZFIN designator faah2amn50 []. […]

Citations

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ZFIN institution(s)
The Institute of Neuroscience, University of Oregon, Eugene, OR, USA
ZFIN funding source(s)
Supported by National Human Genome Research Institute at the US National Institutes of Health [U41 HG002659].

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