Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Investigation into molecular mechanisms behind microbiome and normal neurobehavioral development in zebrafish

ABSTRACT: Changes in resident microbiota may have wide-ranging effects on human health. Previous research found axenic zebrafish (Danio rerio) exhibit hyperactivity at 10 days post fertilization (dpf). This abnormal neurobehavioral response can be prevented with re-colonization of axenic embryos with microbes at 1 dpf. The present study investigated the molecular mechanism behind this effect through RNA-sequencing of pooled 10 dpf larval head tissue from axenic, conventionally colonized controls, and axenic zebrafish recolonized with microbes at 1 dpf.

ORGANISM(S): Danio rerio

PROVIDER: GSE294778 | GEO | 2025/05/30

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Insights into the modes of action of tritium on zebrafish, Danio rerio, early-life stages, using proteomic analyses

Project description:Tritium is an ubiquist radionuclide which can be found in the environment due to natural and anthropogenic activities, particularly in aquatic ecosystems. In this context, tritium effects on aquatic species such as fish have to be characterized. HTO (tritiated water) effects were therefore investigated in zebrafish, Danio rerio, a common model in toxicology and ecotoxicology with a fully sequenced genome. Experiments were conducted on early life stages. Larvae were exposed to 0.4 and 4 mGy/h of HTO until 10 days post fertilization. Tritium internalization was quantified and effects were investigated using a proteomic analysis. The global analysis of the proteome was performed after protein extraction at 7 and 10 dpf on zebrafish eggs exposed from 3 hpf to 10 dpf.

2024-08-29 | PXD022578 | Pride

FACS-Assisted Microarray Profiling Implicates Novel Genes and Pathways in Zebrafish Gastrointestinal Tract Development

Project description:Zebrafish (Danio rerio) gutGFP transgenic embryos [Tg(XlEef1a1:GFP)s854] were collected at 4 time points: 2 days post fertilization (dpf), 3, dpf, 4 dpf, 6 dpf. Embryos were dissociated into single cells and sorted by FACS based on GFP expression. RNA was extracted from the different cell populations (Stratagene), amplified (NuGEN Ovation), and hybridized to Affymetrix Zebrafish GeneChips. Keywords: Time course.

2009-07-10 | GSE12189 | GEO

Investigation into molecular mechanisms behind microbiome and normal neurobehavioral development in zebrafish

Project description:Investigation into molecular mechanisms behind microbiome and normal neurobehavioral development in zebrafish

| PRJNA1251588 | ENA

Transcription profiling of Zebrafish single cell dissected and FACS sorted embryos to investigate gastrointestinal tract development implicates novel genes and pathways

2009-07-19 | E-GEOD-12189 | biostudies-arrayexpress

Zebrafish Cyp1b1 knockout alters eye and brain metabolomic profiles, affecting ocular and neurobehavioral function

Project description:Cytochrome P450 1B1 (CYP1B1) is an enzyme that metabolizes endogenous and xenobiotic compounds. CYP1B1 is thought to be involved in the metabolism of compounds vital to the proper development of the eye. Studies have identified CYP1B1 as a causative gene in the ocular disease primary congenital glaucoma (PCG), however CYP1B1’s role in PCG development and related eye disorders is poorly understood. To explore CYP1B1’s role an in vivo zebrafish (Danio rerio) model was used. This study sought to determine if knocking out CYP1B1 produced an ocular defect similar to PCG and whether this could be distinguished from other neurobehavioral effects. To do this a new CYP1B1 knockout line (wh5) was generated using CRISPR/Cas9 induced deletions truncating the protein before the catalytic domain. Behavior assays, untargeted metabolomics, and RNA sequencing was used to determine the phenotype of the wh5 line. RNA sequencing based transcriptomics was performed on adult eye and brain samples. 95 genes in the eye and 45 genes in the brain were found to be differentially expressed between the genotypes. Untargeted metabolomics analysis was performed on the same tissue type and pathway analysis was performed on the separate data sets. KEGG pathways involved in lipid, steroid, amino acid, and nitrogen metabolism were found to be significantly perturbed. A joint pathway multi-omics analysis was performed introducing gene interactions into the metabolomics pathway analysis. wh5 zebrafish performed significantly different in multiple larval and adult behavior assays, however an ocular defect could not be distinguished from other neurobehavioral phenotypes due to large metabolic and transcriptomic changes in both organs.

2025-04-14 | GSE272589 | GEO

Wild-type Zebrafish subjected to swim-training

Project description:Genome-wide microarray analysis of the effects of swim-training on zebrafish larval development. Zebrafish were subjected to swim-training from 5 days post fertilization (dpf) until 10 dpf. Subsequently, we performed a genome-wide microarray analysis of trained and control fish at 10 dpf. The goal of the project was to investigate the effects of swim-training on the gene expression level during zebrafish larval development

2014-07-17 | GSE42967 | GEO

Lack of de novo phosphatidylinositol synthesis leads to endoplasmic reticulum stress and hepatic steatosis in cdipt-deficient zebrafish

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.

2011-05-09 | GSE17711 | GEO

Epigenome-wide analyis of neurobehavioral variation in preterm infants

Project description:Neonatal molecular biomarkers of neurobehavioral responses (measures of brain-behavior relationships), when combined with neurobehavioral performance measures, could lead to better predictions of long-term developmental outcomes. To this end, we examined whether variability in epigenomic measures from buccal cells were associated with neurobehavioral profiles in a cohort of infants born less than 30 weeks postmenstrual age (PMA) and participating in the Neonatal Neurobehavior and Outcomes in Very Preterm Infants (NOVI) Study (N=536). We tested whether epigenetic age, age acceleration, or DNA methylation (DNAm) levels at individual loci, measured via the Illumina EPIC microarray, differed between infants based on their NICU Network Neurobehavioral Scale (NNNS) profile classifications, ranging from most optimal to atypical. We adjusted for recruitment site, infant sex, PMA, and tissue heterogeneity. Infants with an optimally well-regulated NNNS profile had older epigenetic age compared to other NOVI infants (β1 = 0.201, p-value = 0.026), but no significant difference in age acceleration. In contrast, infants with an atypical NNNS profile had differential methylation at 29 CpG sites (FDR < 10%). Some of the genes annotated to these CpGs included PLA2G4E, TRIM9, GRIK3, and MACROD2, which have previously been associated with neurological structure and function, or with neurobehavioral disorders. These findings contribute to the existing evidence that neonatal epigenetic variations in buccal cells may be informative for infant neurobehavior.

2019-03-26 | GSE128821 | GEO

Effect of swim-training on caudal fin development in zebrafish larvae

Project description:Genome-wide microarray analysis of the effects of swim-training on caudal fin development in zebrafish larvae. Zebrafish were subjected to swim-training from 5 days post fertilization (dpf) until 10 dpf. Subsequently, we performed a genome-wide microarray analysis on the caudal fins of control and trained fish at 10 dpf. The goal of the project was to investigate the effects of swim-training on the gene expression level during caudal fin development in zebrafish larvae.

2014-07-17 | GSE44395 | GEO

Altered gene expression in zebrafish embryos exposed to tert-butylhydroquinone and 2,3,7,8-tetrachlorodibenzo-p-dioxin

Project description:Oxidative stress is an important mechanism of chemical toxicity, contributing to teratogenesis as well as to cardiovascular and neurodegenerative diseases. Developing animals may be especially sensitive to chemicals causing oxidative stress. To assess the response to chemicals at different stages of development, zebrafish (Danio rerio) embryos at 1, 2, 3, 4, 5, and 6 days post-fertilization (dpf) were exposed to 0.1% dimethyl sulfoxide (DMSO), 2 nM 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), or 10 uM tert-butylhydroquinone (tBHQ) for 6 hr. Transcript abundance was assessed by real-time qRT-PCR and microarray (Agilent 22k). By microarray, 1477 probes were significantly different among the DMSO-, tBHQ-, and TCDD-treated embryos at 4 dpf. Of these, 220 were 2-fold or greater up-regulated and 108 were 2-fold or greater down-regulated by tBHQ. For TCDD, 17 probes were 2-fold or greater up-regulated and 6 were 2-fold or greater down-regulated. Genes induced by tBHQ, included genes involved in glutathione synthesis and utilization, signal transduction, and DNA damage / stress response. Keywords: Danio rerio, TCDD, tBHQ, oxidative stress, gene expression

2010-01-01 | GSE10157 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data