Danio rerio
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ABSTRACT:
PROVIDER: PRJNA229146 | ENA |
REPOSITORIES: ENA
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Project description:Brain transcriptome variation among behaviorally distinct strains of zebrafish (Danio rerio)
| PRJNA168578 | ENA
Project description:Domesticated animal populations often show profound reductions in predator avoidance and fear-related behavior compared to wild populations. These reductions are remarkably consistent and have been observed in a diverse array of taxa including fish, birds, and mammals. Experiments conducted in common environments indicate that these behavioral differences have a genetic basis. In this study, we quantified differences in fear-related behavior between wild and domesticated zebrafish strains and used microarray analysis to identify genes that may be associated with this variation. Compared to wild zebrafish, domesticated zebrafish spent more time near the water surface and were more likely to occupy the front of the aquarium nearest a human observer. Microarray analysis of the brain transcriptome identified high levels of population variation in gene expression, with 1,749 genes significantly differentially expressed among populations. Genes that varied among populations belonged to functional categories that included DNA repair, DNA photolyase activity, response to light stimulus, neuron development and axon guidance, cell death, iron-binding, chromatin reorganization, and homeobox genes. Comparatively fewer genes (112) differed between domesticated and wild strains with notable genes including gpr177 (wntless), selenoprotein P1a, synaptophysin and synaptoporin, and acyl-CoA binding domain containing proteins (acbd3 and acbd4). Microarray analysis identified a large number of genes that differed among zebrafish populations and may underlie behavioral domestication. Comparisons with similar microarray studies of domestication in rainbow trout and canids identified sixteen evolutionarily or functionally related genes that may represent components of shared molecular mechanisms underlying convergent behavioral evolution during vertebrate domestication. However, this conclusion must be tempered by limitations associated with comparisons among microarray studies and the low level of population-level replication inherent to these studies. RNA was extracted from the brains of fish from four behaviorally distinct strains of zebrafish and hybridized on Affymetrix microarrays. Brains from 2-5 individual fish of the same sex were pooled and homogenized together, for a total of two biological replicate pools per sex per strain (16 microarrays total).
2012-06-14 | E-GEOD-38729 | biostudies-arrayexpress
Project description:All vertebrates have multiple genes encoding for different CASQ isoforms. Increasing interest has been focused on mammalian and human CASQ genes since mutations of both cardiac (CASQ2) and skeletal (CASQ1) isoforms cause different, and sometime severe, human pathologies Danio rerio (zebrafish) is a powerful model for studying function and mutations of human proteins. In this work expression, biochemical properties and cellular and sub-cellular localization of Danio rerio native CASQ isoforms are investigated. By quantitative PCR three mRNAs were detected in skeletal muscle and one mRNA in heart. Three zebrafish CASQs were identified by mass spectrometry and they share properties with mammalian skeletal and cardiac CASQs. Skeletal calsequestrins were found primarily, but not exclusively, at the sarcomere Z-line level where Terminal Cisternae of Sarcoplasmic reticulum are located.
2015-11-10 | PXD002455 | Pride
Project description: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 understand the genetic changes that accompany behavioral adaptation to domestication. We performed a microarray analysis comparing the midbrain and telencephalon brain regions of male and female adult zebrafish from four populations varying in domestication history (Wild: Nadia (N) and Pargana (P), and Domesticated: Scientific Hatchery (S) and Transgenic Mosaic 1 (T)). We collected 16 samples per brain region (4 samples per zebrafish population, with 1 telencephalon sample missing for the S population). We attempted to maintain equal sex ratios within each zebrafish population, but this was not always possible due to sex biases within some populations.
2014-03-01 | E-GEOD-52512 | biostudies-arrayexpress
Project description:In triplicate for each condition, 12 WT and acbd6 F0 crispant Danio rerio (zebrafish) embryos were incubated with 20 μM YnMyr for 24 h, either between 48-72 hpf or 96-120 hpf. After labelling, zebrafish were washed twice with fresh egg water, deyolked, flash frozen in liquid nitrogen and stored at -80°C until further analysis.
2024-06-16 | PXD043679 | Pride
Project description: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 understand the genetic changes that accompany behavioral adaptation to domestication.
2014-03-01 | GSE52512 | GEO
Project description:In triplicate for each condition, 12 WT and acbd6 F0 crispant Danio rerio (zebrafish) embryos were incubated with 20 μM YnMyr for 24 h, either between 48-72 hpf or 96-120 hpf. After labelling, zebrafish were washed twice with fresh egg water, deyolked, flash frozen in liquid nitrogen and stored at -80°C until further analysis.
2024-06-16 | PXD043676 | Pride
Project description:Chlorothalonil (2,4,5,6-tetrachloroisophthalonitrile) is a broad spectrum fungicide used extensively in agricultural crops . The aim of this study is to analyse the effects of Chorothalonil on the gene expression profiles in zebrafish (Danio rerio), exposed to two concentrations of the fungicide in the water. Nominal concentrations were 1) Low 0.007mg/l (environmentally relevent) and 2) High 0.035mg/ml . A commercial third generation microarray for Danio rerio (Agielnt V3, 4x44k) was used to identify patterns of gene expression in male livers during a 96h toxicological assay.
2015-06-17 | GSE67600 | GEO
Project description:This project aimed at identifying developmental stage specific transcript profiles for catecholaminergic neurons in embryos and early larvae of zebrafish (Danio rerio). Catecholaminergic neurons were labeled using transgenic zebrafish strains to drive expression of GFP. At stages 24, 36, 72 and 96 hrs post fertilization, embryos were dissociated and GFP expressing cells sorted by FACS. Isolated RNAs were processed using either polyA selection and libray generation or NanoCAGE. This is the first effort to determine stage specific mRNA profiles of catecholaminergic neurons in zebrafish.
2012-10-15 | GSE41373 | GEO
Project description:Histidine phosphorylation is a reversible post-translational modification that is known to regulate signal transduction in prokaryotes. In an effort to help elucidate the heretofore hidden vertebrate phosphoproteome, this report presents a global phosphorylation analysis of Danio rerio (zebrafish) larvae. Phosphopeptide enrichment was performed using a TiO2 affinity technique. A total of 68 unique phosphohistidine sites were detected on 63 proteins among 1076 unique phosphosites on 708 proteins. This report provides the first phosphohistidine dataset obtained from zebrafish.
2019-03-21 | PXD012735 | Pride