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| Status |
Public on Sep 09, 2016 |
| Title |
Transcriptomic assessment of PCB-resistance in Atlantic killifish (Fundulus heteroclitus) embryos from a marine Superfund site |
| Organism |
Fundulus heteroclitus |
| Experiment type |
Expression profiling by high throughput sequencing
|
| 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.
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| Overall design |
We performed 454 RNA-sequencing of 6 killifish embryo samples. Four of these were from a pool of 10 days post-fertilization (dpf) embryos from Scorton Creek (Sandwich, MA) and New Bedford Harbor (New Bedford, MA) populations, exposed to either DMSO or PCB126. The remaining two samples were pooled untreated embryos sampled every day from 1 to 15 dpf from the same two populations.
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| Contributor(s) |
Karchner SI, Hahn ME |
| Citation(s) |
21609454 |
| |
| Submission date |
Sep 08, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Sibel Karchner |
| E-mail(s) |
skarchner@whoi.edu
|
| Organization name |
Woods Hole Oceanographic Institution
|
| Department |
Biology
|
| Street address |
45 Water St
|
| City |
Woods Hole |
| State/province |
MA |
| ZIP/Postal code |
02543 |
| Country |
USA |
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| Platforms (1) |
| GPL22406 |
454 GS FLX Titanium (Fundulus heteroclitus) |
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| Samples (6)
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| Relations |
| BioProject |
PRJNA342319 |
| SRA |
SRP087635 |
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