What is The Adult Zebrafish Brain Gene Expression Database?
Zebrafish is a useful model organism in neuroscience. In this database, in situ hybridization data of gene
expression in the brain of adult fish can be viewed and downloaded. The detailed experimental procedures are
described in the following paper. Briefly, 3-5 fish per gene were sampled. Sampled brains were PFA-fixed and
paraffin-embedded, and serial sections of whole brains were prepared. The whole brain of a zebrafish can be
placed on a single glass slide. Each glass slide was subjected to in situ hybridization and scanned with a
NanoZoomer HT slide scanner (Hamamatsu Photonics). All scan data can be viewed and downloaded from the
present database.
Mapped genes
Neuropeptide genes
agrp, asip2b, avp, calca, cart2a, cart2b, cart3a, cart3b, cart4, cart5, ccka, cckb, crha, crhb, gal, galp, gnrh2, gnrh3, grp, kiss1, kiss2, npb, npvf, npy, hcrt, oxt, pdyn, penka, penkb, pmch, pmchl, pomca, pomcb, tac1, tac3a, tac3b, vipa, vipb
Neurotransmitter marker genes
GABAergic neuron marker :gad1a, gad1b, gad2
glutamatergic neuron marker gene: slc17a6a, slc17a6b, slc17a7a, and slc17a7b
To be added
Table data download
All table data in MS Excel format xlsx.zip
- zebrafish telencephalon (Fig 21 expression table.xlsx)
- Comparison of neuropeptide expression patterns in the nuclei of the zebrafish telencephalon. Expression of neuropeptides (green) and neurotransmitter markers (purple) in the olfactory bulb (yellow), dorsal telencephalon (light yellow), ventral telencephalon (light orange), and entopeduncular nucleus (orange) were summarized (expressed = 1, not expressed = 0; for gad and vglut, the one that is expressed more = 1, the one that is expressed less = 0).
- zebrafish pallium and mouse pallium (Fig 22 pallium expression table.xlsx)
- Comparison between zebrafish and mouse telencephalic nuclei based on their neuropeptide expression patterns. Expression of neuropeptides (green) and neurotransmitter markers (purple) in the nuclei of zebrafish (light yellow) and mice (light blue) were extracted from the present ISH results (zebrafish), the Allen Mouse Brain Atlas and previous papers (mouse) and summarized in a table (expressed = 1, not expressed = 0; for Gad and Vglut, the one that is expressed more = 1, the one that is expressed less = 0).
- zebrafish subpallium and mouse subpallium (Fig 22 subpallium expression table.xlsx)
- Comparison between zebrafish and mouse telencephalic nuclei based on their neuropeptide expression patterns. Expression of neuropeptides (green) and neurotransmitter markers (purple) in the nuclei of zebrafish (light yellow) and mice (light blue) were extracted from the present ISH results (zebrafish), the Allen Mouse Brain Atlas and previous papers (mouse) and summarized in a table (expressed = 1, not expressed = 0; for Gad and Vglut, the one that is expressed more = 1, the one that is expressed less = 0).
- zebrafish hyplothalamus (Fig 27 expression table.xlsx)
- The expression of neuropeptides (green) and neurotransmitter markers (purple) in the preoptic area (light yellow) and hypothalamus (orange) is summarized in a table (expressed = 1, not expressed = 0; for Gad and Vglut, the one that is expressed more = 1, the one that is expressed less = 0).
- zebrafish hyplothalamus and mouse hypothalamus (Fig 28 expression table.xlsx)
- Comparison between zebrafish and mouse hypothalamic nuclei based on their neuropeptide expression patterns. Expression of neuropeptides (green) and neurotransmitter markers (purple) in the hypothalamic nuclei of zebrafish (light yellow) and mice (light blue) was extracted from the present ISH results (zebrafish), the Allen Mouse Brain Atlas, and previous papers (mouse) and summarized in a table (expressed = 1, not expressed = 0; for Gad and Vglut, the one that is expressed more = 1, the one that is expressed less = 0).
Publication
Hiraki-Kajiyama T, Miyasaka N, Ando R, Wakisaka N, Itoga H, Onami S, Yoshihara Y. An atlas and database of neuropeptide gene expression in the adult zebrafish forebrain. J Comp Neurol. 2024 Jun;532(6):e25619. doi: 10.1002/cne.25619. PMID: 38831653.
An atlas and database of neuropeptide gene expression in the adult zebrafish forebrain
Towako Hiraki-Kajiyama, Nobuhiko Miyasaka, Reiko Ando, Noriko Wakisaka, Hiroya Itoga, Shuichi Onami, Yoshihiro Yoshihara
bioRxiv 2023.03.29.534505; doi: https://doi.org/10.1101/2023.03.29.534505
Contributors
Imaging contributors
- Towako Hiraki-Kajiyama, Laboratory for Systems Molecular Ethology, Center for Brain Science, RIKEN Center for Brain Science
- Reiko Ando, Support Unit for Bio-Material Analysis, Research Resources Division, RIKEN Center for Brain Science
- Yoshihiro Yoshihara, Laboratory for Systems Molecular Ethology, Center for Brain Science, RIKEN Center for Brain Science
- Nobuhiko Miyasaka, Laboratory for Systems Molecular Ethology, Center for Brain Science, RIKEN Center for Brain Science
- Noriko Wakisaka, Laboratory for Systems Molecular Ethology, Center for Brain Science, RIKEN Center for Brain Science
Database construction contributors
- Hiroya Itoga, Laboratory for Developmental Dynamics, RIKEN Center for Biosystems Dynamics Research
- Shuichi Onami, Laboratory for Developmental Dynamics, RIKEN Center for Biosystems Dynamics Research