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Boston University: Dataset Details, ID=GSE86593

Superfund Research Program

Mechanisms and Impacts of PCB Resistant Fish

Project Leader: Mark E. Hahn (Woods Hole Oceanographic Institution)
Co-Investigators: Sibel I. Karchner (Woods Hole Oceanographic Institution), Neelakanteswar Aluru (Woods Hole Oceanographic Institution)
Grant Number: P42ES007381
Funding Period: 1995-2021

Project-Specific Links

Title: Transcriptomic assessment of PCB-resistance in Atlantic killifish (Fundulus heteroclitus) embryos from a marine Superfund site

Accession Number: GSE86593

Link to Dataset:

Repository: Gene Expression Omnibus (GEO)

Data Type(s): Gene Expression

Experiment Type(s): Array expression profiling by high throughput sequencing

Organism(s): Fundulus heteroclitus

Summary: RNA from PCB-126 exposed 10 days post-fertilization (dpf) embryos were sequenced to characterize the chemical exposure response of killifish from a PCB-resistant population (NBH, New Bedford Harbor, MA, Superfund site) as compared to a reference (SC, Scorton Creek, MA) population. Since the genome sequence was not available, we also performed shot-gun sequencing of RNA from 1-15 dpf embryos sampled every day from both populations to serve as a transcriptome assembly. The results suggest that the NBH fish possess a gene regulatory defect that is not limited to a few target genes. We detected multiple genes that were differentially expressed in these two populations. This study was the first application of pyrosequencing technology to combine transcriptome characterization and gene expression profiling in a marine animal.

Publication(s) associated with this dataset:
  • Oleksiak MF, Karchner SI, Jenny MJ, Franks DG, Mark Welch DB, Hahn ME. 2011. Transcriptomic assessment of resistance to effects of an aryl hydrocarbon receptor (AHR) agonist in embryos of Atlantic killifish (Fundulus heteroclitus) from a marine Superfund site. BMC Genomics 12:263. doi:10.1186/1471-2164-12-263 PMID:21609454 PMCID:PMC3213123
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