Danio rerio
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA351860 | ENA |
REPOSITORIES: ENA
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Project description:Purpose:To investigate the transcriptomic profiles in zebrafish embryos exposed externally to nucleotides at a critical develpomental window (3-7 days post fertilization) determine biological processes and pathways based on differentially expressed gene transcripts using High Throughput Sequencing (HTS). Methods:Total mRNA profiles of 7 dpf zebraifsh embryos after exposure to 10-5M ATP, AMP, adenosine and adenine were generated by deep sequencing, in triplicate, using Illumina HiSeq2500 Results: There were many differentially expressed genes; including ubiquitin-, actin-, and tubulin-related, showing that the cytoskeleton was altered; other DEGs involved with purine binding, specifically guanine, which was expected as the mixture was composed of purines; DEGs involved with GTP binding were also upregulated, suggesting increased cell signaling,
2020-03-23 | GSE97016 | GEO
Project description:MicroRNAs were isolated from wild type (SW and SLW; sapje-wild type littermates, sapje-like-wild type littermates) and sapje and sapje-like fish at 5 and 30 days post fertilization (dpf) Comparison of wildtype and sapje and sapje-like fish at 5 and 30 dpf to identify commonly dysregulated microRNA biosignature
2013-07-01 | GSE40204 | GEO
Project description:Polychlorinated biphenyls (PCBs) are persistent and ubiquitously distributed environmental pollutants. Based on their chemical structure, PCBs are classified into non-ortho substituted and ortho-substituted congeners. Non-ortho-substituted PCBs are structurally similar to dioxin or TCDD (2,3,7,8-tetrachlorodibenzo-p-dioxin) and their mode of action and toxic effects are well established. In contrast, much less is known about the effects of ortho-substituted PCBs. Studies conducted so far have focused on tissue-specific effects but there is limited knowledge about the effects on the whole organism, particularly the sensitive developmental stages in vertebrates. Hence, in this study we investigated the effects of exposure to an environmentally relevant ortho-substituted PCB (2,2’,4,4’,5,5’-hexachlorobiphenyl; PCB153) on zebrafish embryos. We exposed zebrafish embryos to either DMSO (0.1%; solvent control) or three different concentrations of PCB153 (0.1, 1 and 10 μM) from 4 hours post-fertilization (hpf) to 120 hpf. At the end of the exposure, larvae were sampled for determining transcriptional changes (RNA sequencing) and the remaining embryos were maintained in contaminant-free environment. At 7 and 14 days post-fertilization (dpf), zebrafish larvae were assessed for locomotory behavior. We did not observe any overt phenotypes during the exposure period, but observed a spinal phenotype in the 10μM PCB153 treated group starting at 7 dpf. This phenotype was observed in a dose-dependent manner and majority of the embryos with this phenotype died by 14 dpf. RNA sequencing of 5 dpf larvae exposed to PCB153 also revealed dose-dependent changes in gene expression patterns. A total of 633, 2227, and 3378 differentially expressed genes were observed in 0.1, 1 and 10 μM PCB153 treated embryos, respectively. Among these, 301 genes were common to all treatment groups, and KEGG pathway analysis revealed enrichment of genes related to circadian rhythm, FOXO signaling and insulin resistance pathways. We are currently investigating the functions of genes that are uniquely altered by different PCB153 concentrations. Overall, these results suggest that developmental exposure to PCB153, a PCB congener highly prevalent in the environment, targets multiple physiological processes including photoperiod regulation and metabolism. [Funded by NIH P01ES021923 and NSF OCE-1314642].
2017-12-31 | GSE93310 | GEO
Project description:Zebrafish ectonucleoside triphosphate/diphosphohydrolase 5 (entpd5) mutants compared to siblings at 7 dpf
| PRJNA152143 | ENA
Project description:MicroRNAs were isolated from wild type (SW and SLW; sapje-wild type littermates, sapje-like-wild type littermates) and sapje and sapje-like fish at 5 and 30 days post fertilization (dpf) Comparison of wildtype and sapje and sapje-like fish at 5 and 30 dpf to identify commonly dysregulated microRNA biosignature This experiment includes 2 groups per cohort (SW1, 2 vs S1, S2 at 5 and 30 dpf) and (SLW1,2 vs SL1, 2 at 5 and 30 dpf)
2013-07-01 | E-GEOD-40204 | biostudies-arrayexpress
Project description:Zebrafish von Hippel-Lindau (vhl) tumor suppressor mutants compared to siblings at 7 dpf
| PRJNA112035 | ENA
Project description:Zebrafish macrophage stimulating protein (Msp) mutants compared to wild types at 3 and 6 dpf
| PRJNA148945 | ENA
Project description:Gene expression profiling of zebrafish embryos at 5 days post fertilization
| PRJNA248106 | ENA
Project description:Gene expression profiling of zebrafish embryos at 5 days post fertilization [Agilent Arrays]
| PRJNA189203 | ENA
Project description:Gene expression profiling of zebrafish embryos at 5 days post fertilization [Illumina RNA-Seq]
| PRJNA189536 | ENA