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| Status |
Public on Dec 06, 2016 |
| Title |
Skin Transcriptomics of Common Bottlenose Dolphins (Tursiops truncatus) from the Northern Gulf of Mexico and Southeastern U.S. Atlantic Coasts |
| Organism |
Tursiops truncatus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Common bottlenose dolphins serve as sentinels for the health of their coastal environments as they are susceptible to health impacts from anthropogenic inputs through both direct exposure and food web magnification. Remote biopsy samples have been widely used to reveal contaminant burdens in free-ranging bottlenose dolphins, but do not address the health consequences of this exposure. To gain insight into whether remote biopsies can also identify health impacts associated with contaminant burdens, we employed RNA sequencing (RNA-seq) to interrogate the transcriptomes of remote skin biopsies from 116 bottlenose dolphins from the northern Gulf of Mexico and southeastern U.S. Atlantic coasts. Gene expression was analyzed using principal component analysis, differential expression testing, and gene co-expression networks, and the results correlated to season, location, and contaminant burden. Season had a significant impact, with over 30% of genes differentially expressed between spring/summer and winter months. Geographic location exhibited lesser effects on the transcriptome, with 15% of genes differentially expressed between the northern Gulf of Mexico and the southeastern U.S. Atlantic locations. Despite a large overlap between the seasonal and geographical gene sets, the pathways altered in the observed gene expression profiles were somewhat distinct. Co-regulated gene modules and differential expression analysis both identified epidermal development and cellular architecture pathways to be expressed at lower levels in animals from the northern Gulf of Mexico. Although contaminant burdens measured were not significantly different between regions, some correlation with contaminant loads in individuals was observed among co-expressed gene modules, but these did not include classical detoxification pathways. Instead, this study identified other, possibly downstream pathways, including those involved in cellular architecture, immune response, and oxidative stress, that may prove to be contaminant responsive markers in bottlenose dolphin skin.
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| Overall design |
RNA-seq of skin from 116 common bottlenose dolphins.
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| Contributor(s) |
Neely MG, Morey JS, Anderson PE, Balmer BC, Ylitalo GM, Zolman ES, Speakman TR, Sinclair C, Bachman M, Huncik K, Kucklick J, Rosel PE, Mullin KD, Rowles TK, Schwacke LH, VanDolah FM |
| Citation(s) |
28843847 |
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| Submission date |
Dec 06, 2016 |
| Last update date |
Sep 26, 2019 |
| Contact name |
Marion Neely |
| E-mail(s) |
marion.neely@gmail.com
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| Organization name |
National Ocean Services
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| Department |
NCCOS
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| Lab |
Marine Genomics Core Facility
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| Street address |
331 Ft. Johnson Rd
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| City |
Charleston |
| State/province |
SC |
| ZIP/Postal code |
29412 |
| Country |
USA |
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| Platforms (1) |
| GPL21538 |
Illumina HiSeq 2500 (Tursiops truncatus) |
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| Samples (116)
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| Relations |
| BioProject |
PRJNA356411 |
| SRA |
SRP094638 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE90941_RAW.tar |
33.2 Mb |
(http)(custom) |
TAR (of TXT) |
| GSE90941_SE51_NGOM65_RSEM_Genome_FPKM_Matrix.xlsx |
13.2 Mb |
(ftp)(http) |
XLSX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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