Gene expression in the adult zebrafish intestine during starvation and refeeding
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA591019 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR10511874.fastq.gz | Fastqsanger.gz | |||
| SRR10511875.fastq.gz | Fastqsanger.gz | |||
| SRR10511876.fastq.gz | Fastqsanger.gz | |||
| SRR10511877.fastq.gz | Fastqsanger.gz | |||
| SRR10511878.fastq.gz | Fastqsanger.gz |
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Project description:In this RNA-Seq dataset, we describe transcriptomic changes in whole dissected intestinal tracts taken from adult zebrafish that were either fed normally or subjected to a prolonged starvation/refeeding regimen. Analysis of this RNA-Seq data revealed starvation-induced alterations in transcript levels for many genes, including a decrease in lipid metabolism and an increase in innate immune responses. Refeeding for as little as 3 days after starvation was sufficient to restore most transcripts to their baseline pre-starvation levels. These host RNA-Seq results are accompanied by a 16S rRNA gene sequencing dataset from similarly treated adult zebrafish to define changes in intestinal microbiome composition associated with starvation and refeeding.
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Project description:We used microarray analyses in adult female zebrafish (Danio rerio) to identify metabolic pathways regulated by starvation in two key organs that 1) serve biosynthetic and energy mobilizing functions (liver) and 2) consume energy and direct behavioral responses (brain). Starvation affected the expression of 574 transcripts in the liver, indicating an overall decrease in metabolic activity, reduced lipid metabolism, protein biosynthesis and proteolysis, and cellular respiration, and increased gluconeogenesis. Starvation also regulated expression of many components of the Unfolded Protein Response, the first such report in a species other than yeast (Saccharomyces cerevisiae) and mice (Mus musculus). The response of the zebrafish hepatic transcriptome to starvation was strikingly similar to that of rainbow trout (Oncorhynchus mykiss), but very different from common carp (Cyprinus carpio) and mouse. The transcriptome of zebrafish whole brain was much less affected than the liver, with only two differentially expressed genes, both down-regulated. Down-regulation of one of these genes, matrix metalloproteinase 9 (mmp9), suggests increased inhibition of apoptosis (neuroprotection) and decreased restructuring of the extracellular matrix in the brain of starved zebrafish. The low level of response in the transcriptome of whole zebrafish brain agrees with observations that the brain is metabolically protected compared to the rest of the body. Experiment Overall Design: Brain treatments: Starved (21 days) and Control (Fed). Four microarrays per treatment. Experiment Overall Design: Liver treatments: Starved (21 days) and Control (Fed). Five microarrays per treatment. Experiment Overall Design: Data for brain and liver were normalized and analyzed separately because variances of expression differed considerably between the tissues.
2008-06-11 | E-GEOD-11107 | biostudies-arrayexpress
Project description:We used microarray analyses in adult female zebrafish (Danio rerio) to identify metabolic pathways regulated by starvation in two key organs that 1) serve biosynthetic and energy mobilizing functions (liver) and 2) consume energy and direct behavioral responses (brain). Starvation affected the expression of 574 transcripts in the liver, indicating an overall decrease in metabolic activity, reduced lipid metabolism, protein biosynthesis and proteolysis, and cellular respiration, and increased gluconeogenesis. Starvation also regulated expression of many components of the Unfolded Protein Response, the first such report in a species other than yeast (Saccharomyces cerevisiae) and mice (Mus musculus). The response of the zebrafish hepatic transcriptome to starvation was strikingly similar to that of rainbow trout (Oncorhynchus mykiss), but very different from common carp (Cyprinus carpio) and mouse. The transcriptome of zebrafish whole brain was much less affected than the liver, with only two differentially expressed genes, both down-regulated. Down-regulation of one of these genes, matrix metalloproteinase 9 (mmp9), suggests increased inhibition of apoptosis (neuroprotection) and decreased restructuring of the extracellular matrix in the brain of starved zebrafish. The low level of response in the transcriptome of whole zebrafish brain agrees with observations that the brain is metabolically protected compared to the rest of the body. Keywords: starvation study
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Project description:We found that adult zebrafish bearing a homozygous hypomorphic mutation in the sec31a gene (sec31anju221) exhibited overt glycogenic hepatopathy. As an efforts to investigate how hepatic metabolic maladaptation happened in sec31anju221 fish, livers were dissected from the adult zebrafish and DIA-MS was applied.
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