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Wild-type Zebrafish subjected to swim-training

ABSTRACT: 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

ORGANISM(S): Danio rerio

PROVIDER: GSE42967 | GEO | 2014/07/17

SECONDARY ACCESSION(S): PRJNA183953

REPOSITORIES: GEO

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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 Two-condition experiment: control vs trained fish. RNA was isolated from 10 control fish and from 10 trained fish. Subsequently, each sample was labeled with Cy3 and Cy5 in order to correct for dye bias. Control-Cy3 and Trained-Cy5 were hybridized on array 1 and Trained-Cy5 and Control-Cy3 were hybridized on array 2.

2014-07-17 | E-GEOD-42967 | biostudies-arrayexpress

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

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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. Two-condition experiment: control vs trained fish. RNA was isolated from pooled caudal fins of 15 control fish (in duplo: pooled control samples (C2 and C3)) and of 15 trained fish (in duplo: pooled trained samples( T2 and T3)). Subsequently, each pooled RNA sample of control and trained caudal fins was labeled with Cy3 and Cy5 in order to correct for dye bias. We included a technical replicate of the labeled C2 and T2 samples.

2014-07-17 | E-GEOD-44395 | biostudies-arrayexpress

Dynamic Expression of the Zebrafish (Danio rerio) Proteome Across Early Larval Development

Project description:Here, we characterize proteome expression patterns in larval zebrafish at 4-, 7- and 10 dpf using bottom-up shotgun proteomics

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

Project description: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.

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Metabolic and transcriptional adaptations improve physical performance of zebrafish

Project description:Background: Obesity is a worldwide public health problem with increasing prevalence and affects 80% of diabetes mellitus type 2 cases. Zebrafish (Danio rerio) are an established model organism for studying obesity and diabetes including diabetic microvascular complications. We aimed to determine whether physical activity is an appropriate tool to examine training effects in zebrafish and to analyse metabolic and transcriptional processes in trained zebrafish. Methods: A 2- and 8-weeks experimental training phase protocol with adult zebrafish in a swim tunnel system was established. We examined zebrafish basic characteristics before and after training such as body weight, body length and maximum speed and considered overfeeding as an additional parameter in the 8-weeks training protocol. Ultimately, the effects of training and overfeeding on blood glucose, muscle core metabolism and liver gene expression using RNA-Seq were investigated. Results: Zebrafish maximum speed was correlated with body length and was significantly increased after 2 weeks of training. Maximum swim speed further increased after 8 weeks of training in both the normalfed and the overfed groups, but training was found not to be sufficient in preventing weight gain in overfed fish. Metabolome and transcriptome profiling in trained fish exhibited increased blood glucose levels in the short-term and upregulated energy supply pathways in the long-term. Conclusion: Swim training is a valuable tool to study effects of physical activity in zebrafish, which is accompanied by metabolic and transcriptional adaptations.

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Danio rerio

Project description:Wild-type Zebrafish subjected to swim-training

| PRJNA183953 | ENA

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DNA methylation analysis for target regions in swim-up sperm and HRCS.

Project description:Majority of histones are replaced by protamine during spermatogenesis, but small amount of histones are retained in mammalian spermatozoa. Since nucleosomes in spermatozoa influence epigenetic inheritance, it is important how histones are distributed on sperm genome. We have found that the swim-up sperm used in many studies contains about 10% of immature sperm which do not yet complete the histone-to-protamine replacement. We have developed the novel method to purify the histone replacement-completed sperm (HRCS), and to completely solubilize nucleosomes from cross-linked HRCS without MNase digestion. Here, we analyzed H3 binding profiles in total sperm and HRCS by Chromatin IP – sequencing (ChIP-seq) analysis, and DNA methylation profiles in swim-up sperm and HRCS by target bisulfite sequencing (TGSB).

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