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Danio rerio

ABSTRACT: MicroRNA expression changes during zebrafish (Danio rerio) development induced by hexabromocyclododecane

PROVIDER: PRJNA284830 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR2043030.fastq.gz	Fastqsanger.gz
	SRR2040562.fastq.gz	Fastqsanger.gz
	SRR2040572.fastq.gz	Fastqsanger.gz
	SRR2040573.fastq.gz	Fastqsanger.gz
	SRR2040574.fastq.gz	Fastqsanger.gz

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Calsequestrins in skeletal and cardiac muscle from adult Danio rerio.

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

Differential hepatic gene expression in zebrafish (Danio rerio) exposed to the fungicide chlorothalonil reveals estrogenicity

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

Construction of Danio rerio Asymmetrical Maps (DreAM)

Project description:Purpose: Construction of 3D zebrafish spatial transcriptomics data for studying the establishment of AP axis. Methods: We performed serial bulk RNA-seq data of zebrafish embryo at three development points. Using the published spatial transcriptomics data as references, we implemented Palette to infer spatial gene expression from bulk RNA-seq data and constructed 3D embryonic spatial transcriptomics. The constructed 3D transcriptomics data was then projected on zebrafish embryo images with 3D coordinates, establishing a spatial gene expression atlas named Danio rerio Asymmetrical Maps (DreAM). Results: DreAM provides a powerful platform for visualizing gene expression patterns on zebrafish morphology and investigating spatial cell-cell interactions. Conclusions: Our work used DreAM to explore the establishment of anteroposterior (AP) axis, and identified multiple morphogen gradients that played essential roles in determining cell AP positions. Finally, we difined a hox score, and comprehensively demonstrated the spatial collinearity of Hox genes at single-cell resolution during development.

2024-04-08 | GSE262578 | 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 | PXD043679 | Pride

Sequencing of Danio rerio brain from wildtype and Tg-microRNA-sponge animals

Project description:Comparison of gene expression profiles from Danio rerio brain of wiltype and Tg-microRNA-sponge animals. The RNA-seq data comprise 3 groups. Jena Centre for Systems Biology of Ageing - JenAge (www.jenage.de)

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2024-06-16 | PXD043676 | Pride

Transcriptional responses of the zebrafish (Danio rerio) brain to acute sodium selenite supplementation.

Project description:The possible benefits of selenium (Se) supplementation are currently under investigation for prevention of certain cancers and treatment of neurological disorders. Little is known concerning the response of the brain to increased dietary Se under conditions of Se sufficiency, despite the majority of Se supplementation trials occurring in healthy subjects considered Se sufficient. We evaluated the transcriptional response of the zebrafish (Danio rerio) brain to supplementation with nutritionally relevant levels of dietary Se (sodium selenite) during conditions of assumed Se sufficiency. We used a microarray approach to analyze the global gene expression response of the brain to dietary Se supplementation for 14 days. The experiment used Affymetrix microarrays to compare whole brain RNA from 8 adult zebrafish (Danio rerio) fed a diet with control selenium levels (1.4ppmSe) and 8 fed a diet supplemented with sodium selenite (5.6ppmSe) for 14 days, and with an equal sex ratio within each diet.

2013-02-26 | E-GEOD-44623 | biostudies-arrayexpress

Differential hepatic gene expression in zebrafish (Danio rerio) exposed to the fungicide chlorothalonil reveals estrogenicity

2015-06-17 | E-GEOD-67600 | biostudies-arrayexpress

Zebrafish (Danio rerio) catecholaminergic neuron RNA-seq based transcript profiles

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

Danio rerio

Project description:microRNA expression during early zebrafish development

| PRJNA92137 | ENA