Ontology highlight
ABSTRACT:
PROVIDER: PRJNA814759 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Zebra fish (Danio rerio) larvae exposure at Cd or Cu Raw sequence reads
| PRJNA793298 | ENA
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
Project description:comparison of miRNA expression in zebrafish tissues Keywords = miRNA Keywords = microRNA Keywords = zebrafish Keywords = Danio rerio Keywords = development Keywords: other
2005-07-05 | GSE2628 | GEO
Project description:Bekaert2012 - Reconstruction of D.rerio Metabolic Network
Danio rerio
metabolic model accounting for subcellular compartmentalisation (ZebraGEM)
This SBML representation of the D. rerio
(zebrafish) metabolic network is made available under the Creative Commons Attribution-Share Alike 3.0 Unported Licence (see www.creativecommons.org
).
This model is described in the article:
Reconstruction of Danio rerio Metabolic Model Accounting for Subcellular Compartmentalisation.
Bekaert M.
PLoS One. 2012;7(11):e49903.
Abstract:
Plant and microbial metabolic engineering is commonly used in the production of functional foods and quality trait improvement. Computational model-based approaches have been used in this important endeavour. However, to date, fish metabolic models have only been scarcely and partially developed, in marked contrast to their prominent success in metabolic engineering. In this study we present the reconstruction of fully compartmentalised models of the Danio rerio (zebrafish) on a global scale. This reconstruction involves extraction of known biochemical reactions in D. rerio for both primary and secondary metabolism and the implementation of methods for determining subcellular localisation and assignment of enzymes. The reconstructed model (ZebraGEM) is amenable for constraint-based modelling analysis, and accounts for 4,988 genes coding for 2,406 gene-associated reactions and only 418 non-gene-associated reactions. A set of computational validations (i.e., simulations of known metabolic functionalities and experimental data) strongly testifies to the predictive ability of the model. Overall, the reconstructed model is expected to lay down the foundations for computational-based rational design of fish metabolic engineering in aquaculture.
This model is hosted on BioModels Database
and identified by: MODEL1204120000
.
To cite BioModels Database, please use: BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. PMID: 20587024
.
To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to [CC0 Public Domain Dedication>http://creativecommons.org/publicdomain/zero/1.0/] for more information.
2005-01-01 | MODEL1204120000 | BioModels
Project description:Cronobacter (C.) is an important emerging opportunistic foodborne pathogen representing significant cause of mortality in neonatal patients with bacteremia and meningitis. Knowledge on the pathobiology of Cronobacter mediated meningitis has to a large extend been explored using in vitro models. To explore the innate immune response against the neonatal sepsis/meningitis causing isolate C. turicensis z3032 in vivo, zebrafish larvae (Danio rerio) were used as infection model. Following establishment of infection in zebrafish larvae with z3032, dual RNA-sequencing of host-pathogen was undertaken to profile RNA expression simultaneously in the pathogen and the head region of the zebrafish host.
2024-06-28 | GSE236313 | GEO
Project description:cdipt is an essential gene in the synthesis of phosphatidylinositol (PtdIns) in the zebrafish, Danio rerio. The zebrafish mutant cdipt^hi559Tg (ZL782) carries a retroviral insertion which inactivates cdipt. Homozygous mutants exhibit hepatocellular endoplasmic reticulum (ER) stress and non-alcoholic fatty liver disease (NAFLD) pathologies at 5 days post fertilization (dpf). This study reveals a novel link between PtdIns, ER stress, and steatosis. We compared whole animal gene expression profiles of hi559 mutant larvae with phenotypically wild type larvae from a heterozygote incross in triplicate.
2011-05-09 | E-GEOD-17711 | biostudies-arrayexpress
Project description:Zebeafish yquem harbors a mutation in the gene encoding uroporphyrinogen decarboxylase (UROD), the fifth enzyme in heme biosynthesis, and was established as a vertebrate model for human hepatoerythropoietic porphyria (HEP). In an effort to investigate the unknown aspects of UROD deficiency pathogenesis, we used a 14,000-oligonucleotide-gene microarray to determine differentially expressed genes in yquem/urod (-/-) and wild type control zebrafish larvae. Keywords: zebrafish, Danio rerio, wild-type yquem, urod, porphyria
2007-08-03 | GSE8651 | GEO
Project description:Effect of 5.4 ppm polycyclic aromatic hydrocarbons (PAHs) and 18.2 ppm alkylphenols (APs) on gene expression in adult Zebrafish (Danio rerio) liver after 1 and 7 weeks of water-borne exposure.
2008-12-11 | E-MEXP-1685 | biostudies-arrayexpress
Project description:Homozygous masterblind (mbl-/-) zebrafish exhibit reduced or absent eyes and telecephalon, and the expansion of the diencephalic fates to the front of the brain. A missense mutation in the GSK3-binding domain of zebrafish axin1, a scaffolding protein in the Wnt signaling pathway, results in the mbl phenotype. In an effort to identify and study the genes affected by Wnt signaling, we used a 14,000-oligonucleotide-gene microarray to determine differentially expressed genes in mbl/axin1 (-/-) and wild type control zebrafish embryos and larvae. Keywords: zebrafish, Danio rerio, wild-type mbl, axin1, development
2007-04-27 | GSE6142 | 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