Danio rerio
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ABSTRACT:
PROVIDER: PRJNA141119 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:To gain a better understanding of the diurnal variation in gene expression, we analyzed the changes in gene expression in the eye of zebrafish. Dual color oligonucleotide microarrays were used to compare total RNA harvested from eyes of adult zebrafish at midday and midnight. Statistical analyses identified 44 genes which showed significant, 2-fold or more change; 26 genes showed decreased expression at midnight (D/L ≤ 0.5) and 18 genes showed increased expression at midnight (D/L ≥ 2). Seven genes were further analyzed using qPCR. The results of qPCR identified AANAT, Mel1a1, Mel1a3, Mel1b1, Mel1b2 and Melc as genes that showed significant change in expression at dawn, dusk, midday and midnight. These results suggest that expression of melatonin receptors is subject to diurnal regulation. Wild-type ZDR zebrafish (Danio rerio) were obtained from Animal Wonders, San Marcos, TX, and Aquatica Tropicals, Plant City, FL. Fish were conditioned on a 12 hour light/dark cycle for a minimum of 14 days before use. The design of this analysis compared the experimental to the control: midnight samples were used as experimental and midday as control. Samples were collected in triplicate per time point with each replicate representing total RNA pooled from 9 fish. Dual-color microarray was used to compare the midnight and midday samples. A statistically significant (p-value ≤ 0.05) and 2-fold or more change in an experimental sample as compared to a control indicated an up- or down-regulation in gene expression. Supplementary files: In Complete processed data file, "x" marked spots show intensities of less than 1000. In Intensity trimmed data file, all genes with signal intensities of less than 1000 in all triplicate time points were removed from the analysis.
2012-05-09 | E-GEOD-29696 | biostudies-arrayexpress
Project description:To gain a better understanding of the diurnal variation in gene expression, we analyzed the changes in gene expression in the eye of zebrafish. Dual color oligonucleotide microarrays were used to compare total RNA harvested from eyes of adult zebrafish at midday and midnight. Statistical analyses identified 44 genes which showed significant, 2-fold or more change; 26 genes showed decreased expression at midnight (D/L ≤ 0.5) and 18 genes showed increased expression at midnight (D/L ≥ 2). Seven genes were further analyzed using qPCR. The results of qPCR identified AANAT, Mel1a1, Mel1a3, Mel1b1, Mel1b2 and Melc as genes that showed significant change in expression at dawn, dusk, midday and midnight. These results suggest that expression of melatonin receptors is subject to diurnal regulation.
2012-05-10 | GSE29696 | GEO
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: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:Brain transcriptome variation among behaviorally distinct strains of zebrafish (Danio rerio)
| PRJNA168578 | ENA
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:Natural Variation in Fish Transcriptomes: Comparative Analysis of the Zebrafish (Danio rerio)
| PRJNA257740 | ENA
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