Danio rerio
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA301459 | ENA |
REPOSITORIES: ENA
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Project description:Purpose: The goals of this study are to investigate the toxic effects and molecular mechanisms of GO exposure in adult zebrafish liver by transcriptome profiling (RNA-seq) Methods: Liver mRNA profiles of three-month-old control (CK) and GO-exposed (GO) zebrafish were generated by deep sequencing, in triplicate, using Illumina Hiseq X ten. The sequence reads that passed quality filters were analyzed at the gene level with two methods: RSEM and HISAT followed by Ballgown. qRT-PCR validation was performed using SYBR Green assays Results: Using an optimized data analysis workflow, we mapped about 30 million sequence reads per sample to the zebrafish genome (GRCz11) and identified 43,106 genes in the livers of CK and GO zebrafish with RSEM and HISAT2 workflow. RNA-seq data confirmed stable expression of 10 known housekeeping genes, and 6 of these were validated with qRT-PCR. Approximately 0.7% of the genes showed differential expression between the CK and GO liver, with a fold change ≥1.5 and p value <0.05. Hierarchical clustering of differentially expressed genes uncovered several genes that may contribute to function in liver inflammation and lipid disorder. Conclusions: Our study represents the detailed analysis of zebrafish liver transcriptomes after GO exposure, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that steroid hormone biosynthesis, lipoprotein metabolic process and PPAR signaling pathway were signifificantly enriched. Most of the lipid metabolism genes were down-regulated while majority of the immune genes were up-regulated after GO treatment.
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Project description:Microarray analysis in the zebrafish liver and telencephalon after exposure to low concentration of 17a-EE2
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Project description:Compared to other fish models, miRNAs are currently most extensively studied and identified in zebrafish. Approximately 415 dre-miRNAs have been identified and several articles have studied some aspect of miRNA function in zebrafish such as their role in basic development and in disease pathways. However, this field of research is in its infancy and the function of several dre-miRNAs, as well as their tissue-specific expression profile, are yet to be defined. In this study, the liver and gut were dissected (wildtype/untreated fish), total and small RNA were extracted, mRNA and miRNA libraries constructed and subjected to high throughput sequencing (HTS) using standard approaches. We carried out differential expression (DE) analysis and compared liver miRNA expression to gut using established bioinformatics pipelines. Through bioinformatics analysis, known and putative novel miRNAs were identified. Finally, we constructed a “miRNA matrix” that connects both total RNA-Seq and miRNA-Seq.
2018-12-26 | GSE108436 | GEO
Project description:Pharmaceutical chemicals used in human medicine are released into surface waters via municipal effluents and pose a risk for aquatic organisms. Among these substances are selective serotonin reuptake inhibitors (SSRIs) which can affect aquatic organisms at sub ppb concentrations. To better understand biochemical pathways influenced by SSRIs, evaluate changes in the transcriptome, and identify gene transcripts with potential for biomarkers of exposure to SSRIs; larval zebrafish Danio rerio were exposed (96 h) to two concentrations (25 and 250 µg/L) of the SSRIs, fluoxetine and sertraline, and changes in global gene expression were evaluated (Affymetrix GeneChip® Zebrafish Array). Significant changes in gene expression (>=1.7 fold change, p<0.05) were determined with Partek® Genomics Suite Gene Expression Data Analysis System and ontology analysis was conducted using Molecular Annotation System 3. The number of genes differentially expressed after fluoxetine exposure was 288 at 25 µg/L and 131 at 250 µg/L; and after sertraline exposure was 33 at 25 µg/L and 52 at 250 µg/L. Five genes were differentially regulated in all treatments relative to control, suggesting that both SSRIs share some similar molecular pathways. Among them, expression of the gene coding for FK506 binding protein 5 (FKBP5), which is annotated to stress response regulation, was highly down-regulated in all treatments (results confirmed by qRT-PCR). Gene ontology analysis indicated that regulation of stress response and cholinesterase activity were critical functions influenced by these SSRIs, and suggested that changes in the transcription of FKBP5 or acetylcholinesterase could be useful biomarkers of SSRIs exposure in wild fish.
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