Zebrafish brain

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Unknown (2360)
Genomics (482)
Transcriptomics (409)
Proteomics (61)
Methylation profiling (6)
Other (6)
Metabolomics (3)

Organisms

Danio rerio (337)
Homo sapiens (63)
Mycobacterium tuberculosis SP7 (52)
Mycobacterium tuberculosis SP10 (52)
Mycobacterium tuberculosis SP13 (52)
Mycobacterium tuberculosis SP22 (52)
Chlamydomonas reinhardtii (52)
Enterococcus mundtii CRL35 (52)
Mus musculus (34)
Rattus norvegicus (5)
Oncorhynchus mykiss (3)
Caenorhabditis elegans (3)
Amphimedon queenslandica (2)
Drosophila melanogaster (2)
Dicentrarchus labrax (2)
Esox lucius (1)
Hypsibius dujardini (1)
Mnemiopsis leidyi (1)
Megalobrama amblycephala (1)
Sinocyclocheilus anophthalmus (1)
Pimephales promelas (1)
Strongylocentrotus purpuratus (1)
Nothobranchius furzeri (1)
Platynereis dumerilii (1)
Danio albolineatus (1)
Nematostella vectensis (1)
Xenopus laevis (1)
Arabidopsis thaliana (1)
Branchiostoma lanceolatum (1)
feces metagenome (1)

Organisms

Danio rerio (281)
Homo sapiens (27)
Mus musculus (15)
Dicentrarchus labrax (2)
Pimephales promelas (2)
Rattus norvegicus (2)
Teleostei (1)
Danionella cerebrum (1)
Branchiostoma lanceolatum (1)
Megalobrama amblycephala (1)
Caenorhabditis elegans (1)
feces metagenome (1)

Repository

ENA (444)
geo (282)
biostudies-arrayexpress (163)
pride (52)
EGA (14)
PAXDB (4)
iProX (2)
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MetabolomicsWorkbench (1)
PeptideAtlas (1)

Tissue

Brain (31)
Cell culture (5)
Cerebrospinal fluid (3)
Embryo (3)
Fibroblast (3)
Liver (3)
Eye (2)
Skin (2)
Muscle (2)
Heart (2)
Whole body (2)
Kidney (2)
Heart (1)
Brain (1)
Kidney (1)
Muscle (1)
Liver (1)
Oligodendrocyte (1)
Endosperm (1)
Motor neuron (1)
Hippocampus (1)
Intestine (1)
Retina (1)
Flower bud (1)
Flower (1)
JURKAT cell (1)
Cotyledon (1)
Egg (1)
Ovary (1)
Bone marrow (1)

Disease

Marinesco-Sjogren syndrome (2)
Machado-Joseph disease (2)
Amyotrophic lateral sclerosis (2)
Heart disease (1)
Syndromic intellectual disability (1)
Neurological dysfunction (1)
Huntington Disease (1)
Mixed disorder as reaction to stress (1)
Myocardial ischemia (1)
Disease free (1)

Technology Type

Mass Spectrometry (53)
Shotgun proteomics (30)
Bottom-up proteomics (13)
Data-dependent acquisition (6)
Top-down proteomics (5)
Gel-based experiment (4)
SWATH MS (3)
Affinity purification coupled with mass spectrometry proteomics (3)
MSE (2)
Data-independent acquisition (2)
Illumina HiSeq 2000 (ILLUMINA), Illumina HiSeq 1500 (ILLUMINA) (1)
ILLUMINA, Illumina HiSeq 2000 (1)
Illumina HiSeq 2000 (1)
Illumina HiSeq 2000, ILLUMINA (1)
Mass spectrometry assay (1)
Mass spectrometry (1)
ESI (1)
All-ion fragmentation (1)
HDMSE (1)

Instrument Platform

Illumina NovaSeq 6000 (6)
Thermo ltq (2)
STAR v2.5.3a, rpkmforgenes, RSeQC 2.6.1 (1)
Illumina Nextera XT index kits (Set A–D) (1)
Oligo(dT) primer and SuperScript II reverse transcriptase (ThermoFisher Scientific), TapeStation 4200 or 2100 Bioanalyzer with a DNA High Sensitivity chip (Agilent Biotechnologies) (1)
Aria III (BD Biosciences) (1)
PromethION (1)
Illumina HiSeq 4000 (1)
Intel Xeon E5-2660 (128G RAM) (1)
Illumina Genome Analyzer IIx (1)
ScanArray Express HT [PerkinElmer] (1)
Affymetrix Fluidics Station 400 (1)
Axon GenePix 4000B scanning hardware (1)
Ion Torrent Proton (1)
GenePix 4000B (1)
HiSeq X Ten (1)
NextSeq 550 (1)
Illumina HiSeq 2500 (1)
Illumina HiSeq 2000 (1)
Illumina HiSeq 3000 (1)
Illumina HiSeq 4000 (1)
Orbitrap Fusion ETD (1)
LTQ Orbitrap Elite (1)
Liquid Chromatography MS - alternating - hilic (1)
Liquid Chromatography MS - positive - reverse phase (1)
Liquid Chromatography MS - negative - reverse phase (1)
Agilent Q-ToF (1)
4800 MALDI TOF/TOF Analyzer (1)

Publication Date

2025 (46)
2026 (43)
2024 (37)
2016 (34)
2014 (34)
2020 (31)
2018 (27)
2017 (26)
2019 (25)
2015 (24)
2010 (24)
2023 (23)
2021 (20)
2013 (20)
2012 (20)
2022 (19)
2008 (16)
2011 (14)
2009 (12)
2007 (7)
2005 (3)
2004 (1)

UNIPROT ID/AC

Q6DGM9_DANRE (4)
Q6P5L2_DANRE (4)
OPA1_DANRE (4)
A0A2R8QUY1_DANRE (4)
Q4G5V7_DANRE (4)
DHTK1_DANRE (4)
Q4V8S5_DANRE (4)
Q5RH04_DANRE (4)
F1RBH3_DANRE (4)
F5H8N4_DANRE (4)
F1QTF0_DANRE (4)
F1Q6F0_DANRE (4)
E7F8G7_DANRE (4)
DHSDB_DANRE (4)
Q6IQT9_DANRE (4)
A0A0R4IBT7_DANRE (4)
E7FD66_DANRE (4)
Q502P6_DANRE (4)
Q6P5K6_DANRE (4)
Q7ZVT2_DANRE (4)
Q6PBW8_DANRE (4)
Q1LUP1_DANRE (4)
F6NP87_DANRE (4)
A0A0R4IH79_DANRE (4)
F1QFQ6_DANRE (4)
PRV2_DANRE (4)
Q7T334_DANRE (4)
Q4V918_DANRE (4)
F1QR17_DANRE (4)
Q5RKM3_DANRE (4)

ENSEMBL ID

ENSDARP00000124852 (1)
ENSDARP00000105472 (1)
ENSDARP00000067210 (1)
ENSDARP00000065419 (1)
ENSDARP00000033497 (1)
ENSDARG00000096253 (1)
ENSDARG00000095094 (1)
ENSDARG00000079161 (1)
ENSDARG00000076712 (1)
ENSDARG00000076081 (1)
ENSDARG00000074581 (1)
ENSDARG00000074197 (1)
ENSDARG00000074183 (1)
ENSDARG00000073822 (1)
ENSDARG00000070780 (1)
ENSDARG00000069501 (1)
ENSDARG00000068989 (1)
ENSDARG00000068477 (1)
ENSDARG00000068083 (1)
ENSDARG00000067820 (1)
ENSDARG00000067585 (1)
ENSDARG00000063527 (1)
ENSDARG00000063299 (1)
ENSDARG00000062957 (1)
ENSDARG00000061570 (1)
ENSDARG00000061117 (1)
ENSDARG00000058875 (1)
ENSDARG00000058601 (1)
ENSDARG00000058248 (1)
ENSDARG00000057770 (1)

Metabolite Name

Carpropamid (2)
Primisulfuron-methyl (2)
Isocorynoxeine (2)
Trp-Cys (2)
Pipamperone (2)
Val-Gly-Val (2)
Enterostatin human (2)
Metamitron (2)
Platencin (2)
Aminocyclopyrachlor (2)
Cys-Gln (2)
Trp-Trp-Arg (2)
Ser-Val-Arg (2)
Oleyloxyethylphosphorylcholine (2)
L-Histidinol phosphate (2)
Indanofan (2)
His-Thr (2)
Flumethasone pivalate (2)
Ferrichrome (2)
Defluoroatorvastatin (2)
Bifenox (2)
Arg-Phe-Lys (2)
Amphotericin b (2)
Ala-Glu-Arg (2)
Imazosulfuron (2)
Arg-Ser-Arg (2)
Becatecarin (2)
Beclomethasone dipropionate (2)
Tandutinib (2)
Nintedanib (2)

First Public Date

2025 (75)
2026 (53)
2024 (52)
2014 (46)
2020 (44)
2023 (35)
2022 (32)
2018 (25)
2017 (23)
2019 (21)
2021 (18)
2015 (8)
2016 (6)
2013 (6)

Modification

Not available (3)
57.0215 (1)
15.9949 (1)

Study type

Transcription profiling by array (106)
RNA-seq of coding RNA (28)
Unknown experiment type (5)
ChIP-seq (4)
Methylation profiling by high throughput sequencing (4)
RNA-seq of non coding RNA (4)
RNA-seq of coding RNA from single cells (3)
ChIP-chip by tiling array (2)
Animal - High-throughput sequencing (2)
Other (2)
Animal - Single-cell sequencing (1)
RIP-seq (1)
MicroRNA profiling by array (1)

Release Date

2022 (260)
2024 (230)
2025 (228)
2021 (227)
2023 (198)
2020 (193)
2019 (168)
2017 (139)
2018 (132)
2016 (117)
2015 (115)
2014 (96)
2012 (81)
2013 (76)
2011 (57)
2010 (49)
2009 (35)
2008 (35)
2026 (30)
2007 (25)
2006 (12)
2004 (6)
2005 (4)
2002 (3)
2003 (2)
2000 (2)
1997 (2)
1999 (1)

Lab affiliation

CSIR-CCMB (3)
1 Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Auguste-Piccard-Hof 1, 8093 Zurich, Switzerland 2 Faculty of Science, University of Zurich, Zurich, Switzerland (2)
Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto (2)
Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, London, W12 0BZ, UK The Francis Crick Institute, London, NW1 1AT, UK (2)
Michigan State University (2)
Department Neurobiology and Molecular Medicine, IRCCS Fondazione Stella Maris, 56128 Pisa, Italy (1)
Department of Chemistry, Imperial College London, Molecular Research Science Hub, 80 Wood Lane, London W12 0BZ, United Kingdom. The Francis Crick Institute, 1 Midland Road, London NW1 1AT, United Kingdom. (1)
Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., Otto-Hahn-Str. 6b, 44227 Dortmund, Germany. Tel: ++49-231-13924232; Fax: ++49-231-13924850 (1)
Daglig leder, PROMEC Institutt for klinisk og molekylær medisin lars.hagen@ntnu.no 73598508 72573342 Laboratoriesenteret, 231.04.008, Øya, Erling Skjalgssons gate 1 PROMEC webpages, Norway (1)
Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., Otto-Hahn-Str. 6b, 44227 Dortmund, Germany. Tel: ++49-231-13924232; Fax: ++49-231-13924850 (1)
Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC, UMR 7178, 67000 Strasbourg, France (1)
Department of Environmental and Global Health, College of Public Health and Health Profession, University of Florida, Gainesville, FL (1)
DIMEVET- Unversità degli Studi di Milano (1)
National Institute for Health Research (NIHR) Biomedical Research Centre at Moorfields Eye Hospital NHS Foundation Trust and UCL Institute of Ophthalmology, London, EC1V 9EL (1)
Department of Translational Neuroscience, University Medical Center Utrecht Brain Center, Utrecht University, Universiteitsweg 100, 3584 CG, Utrecht, The Netherlands (1)
CSIR-Indian Institute of chemical Technology (1)
Dipartimento di medicina veterinaria (1)
University of Sheffield (1)
Centro de Referencia para Lactobacilos (CERELA)-CCT NOA Sur- CONICET (1)
Department of Veterinary Medicine and Animal Sciences (DIVAS) CRC Innovation for Well-Being and Environment (I-WE) University of Milan Via dell' Università, 6 - 26900 Lodi, Italy (1)
Proteomics Group Max-Planck-Institute of Experimental Medicine Hermann-Rein-Str. 3 37075 Goettingen, Germany (1)
Laboratory of Applied Proteome Analyses, Institute of Animal Physiology and Genetics of the Czech Academy of Sciences, Libechov, Czech Republic (1)
Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905 (1)
Proteomics Platform, SFR Necker INSERM US24, Université Paris Cité, 160 rue de Vaugirard, 75015 Paris, France (1)
Proteomics platform Necker, Université de Paris - Structure Fédérative de Recherche Necker, INSERM US24/CNRS UMS3633, Paris 75015, France (1)
MPI of Biophysics and MPI for Brain Research, Frankfurt am Main, Germany (1)
Department of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, Michigan 48824, USA (1)
Quantitative Biosciences Institute (QBI), San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA;Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA (1)
2IDAEA-CSIC, Jordi Girona 18, 08034, Barcelona, Spain (1)
Department of Pathology, Microbiology, and Immunology;Vanderbilt Institute for Infection, Immunology, and Inflammation. Vanderbilt University Medical Center, Nashville, TN USA (1)

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Metabolomic Responses to Circadian Rhythm Disruption in Zebrafish

Circadian rhythms are essential biological oscillators that synchronize physiological processes, cellular homeostasis, and systemic metabolism with the Earth's natural 24-hour light-dark cycle. While circadian rhythm disruption (CRD) is highly prevalent in modern society due to factors such as sh...

2026-06-23 | MTBLS14815 | MetaboLights

Spatially-Resolved Top-Down Proteomics of Zebrafish Brain Using Capillary Zone Electrophoresis-Tandem Mass Spectrometry

Understanding region-specific proteoform profiles in the brain is crucial for deciphering neural function and identifying potential therapeutic targets. Here, we present a comprehensive label-free quantitative top-down proteomics (TDP) analysis of distinct zebrafish brain regions using capillary zon...

ORGANISM(S): Danio rerio (Zebrafish) (Brachydanio rerio)

2026-06-08 | PXD070925 | Pride

A detailed proteomic analysis of plasma membrane from zebrafish brain

The brain plasma membrane proteome represents the major subsets of signaling proteins and promising drug targets though often understudied due to traditional experimental difficulties. Here we report a comprehensive dataset of the proteins identified in the highly enriched plasma membrane of zebrafi...

ORGANISM(S): Danio rerio (Zebrafish) (Brachydanio rerio)

2018-07-05 | PXD004209 | Pride

Zebrafish brain Membrane proteome

Gene expression changes in the female zebrafish (Danio rerio) brain in response to acute exposure to methylmercury

Methylmercury (MeHg) is a potent neurotoxin and endocrine disruptor that accumulates in aquatic systems. Previous studies have shown suppression of hormone levels in both male and female fish, suggesting effects on gonadotropin regulation in the brain. We investigated the gene expression profile in ...

ORGANISM(S): Danio rerio

2010-09-30 | E-GEOD-22662 | biostudies-arrayexpress

Quantification of brain, muscle, and liver using large SWATH-spectral library

Sequential window acquisition of all theoretical mass spectra (SWATH-MS) requires a spectral library to extract quantitative measurements from the mass spectrometry data acquired in data-independent acquisition mode (DIA). Large combined spectral libraries containing SWATH assays have been generated...

ORGANISM(S): Danio rerio (Zebrafish) (Brachydanio rerio)

2018-12-18 | PXD010869 | Pride

Brain Liver Zebrafish Muscle

Transcriptomic comparison between brain regions of behaviorally distinct wild and domesticated zebrafish (Danio rerio) populations

Zebrafish populations recently collected from the wild differ from domesticated populations in anxiety-related behaviors. We measured anxiety-related behaviors in wild and domesticated zebrafish populations and performed a multi-brain region transcriptional comparison using microarrays to try to und...

ORGANISM(S): Danio rerio

2014-03-01 | E-GEOD-52512 | biostudies-arrayexpress

Transcription profiling by array of adult zebrafish control and post-lesion retina to investigate the molecular determinants of retinal regeneration in adult vertebrate

Purpose: Investigate the molecular determinants of retinal regeneration in adult vertebrates by analyzing the gene expression profiles of control and post-lesion retina of adult zebrafish, a system that regenerates following injury. Methods: Gene expression profiles of zebrafish retina and brain wer...

ORGANISM(S): Danio rerio

2005-09-16 | E-GEOD-3303 | biostudies-arrayexpress

Top-down proteomics study of aging and sexual dimorphism of zebrafish brains

Here, we present the first example of studying the aging and sexual dimorphism of brains using the zebrafish (Danio rerio) model organism by mass spectrometry (MS)-based quantitative top-down proteomics (TDP). We measured the proteoforms in male and female zebrafish brains across three ages (6, 16, ...

ORGANISM(S): Danio rerio (Zebrafish) (Brachydanio rerio)

2026-01-12 | PXD060426 | Pride

Central nervous system aging proteoform identification zebrafish

Transcriptomic effects of GLUT2 knock-down in zebrafish embryos

Glucose transporter 2 (GLUT2) is a key player in the regulation of glucose dynamics in organs central to metabolism, namely the liver, pancreas and intestine In humans, mutations of the GLUT2 gene (Fanconi-Bickel syndrome) cause important defects in glucose homeostasis. Although GLUT2 has been studi...

ORGANISM(S): Danio rerio

2014-12-23 | E-GEOD-57836 | biostudies-arrayexpress

Zebrafish synaptic proteome - Evolution of complexity in the zebrafish synapse proteome

The proteome of human brain synapses is highly complex and mutated in over 130 diseases. This complexity arose from two whole genome duplications early in the vertebrate lineage. Zebrafish are used in modelling human diseases, however its synapse proteome is uncharacterised and whether the teleost-s...

ORGANISM(S): Danio rerio (Zebrafish) (Brachydanio rerio) Mus musculus (Mouse)

2017-03-06 | PXD005630 | Pride

Synapse Zebrafish Evolution

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