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| Status |
Public on Jul 01, 2018 |
| Title |
Novel applications of next generation sequencing tools to assess the health of Steller sea lion (Eumetopias jubatus) populations |
| Organism |
Eumetopias jubatus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Some rookeries of the western distinct population segment (WDPS) of Steller sea lions (Eumetopias jubatus) in the Aleutian Islands (Alaska, USA) have experienced continued declines since the initial collapse of the population in the 1970-1980s. Several theories have been put forward to explain the decline and lack of subsequent recovery including predation, nutritional stress, contaminants, and infectious disease agents, but thus far a primary cause has not been identified. Examining gene expression profiles of organisms has been promoted as a way to assess several health indicators related to toxicoses, infection, and nutritional stress using recent advances in metagenetics (next-generation sequencing) analyses. Next-generation sequencing may provide a more refined and adaptable method of investigating sea lion health under difficult research field collections. Here we suggest that the application of next-generation sequencing tools has the potential to evaluate the transcriptomic (gene expression) profile of animals from declining rookeries. We show that high quality RNA can be obtained from wildlife populations despite logistically challenging field conditions. We compared RNA expression in whole blood using whole transcriptome sequencing (RNA-Seq) among animals with relatively high concentrations of total mercury ([THg]) to animals with lower concentrations. There did not appear to be significant changes in gene expression in animals with high [THg] in whole blood, despite some animals having concentrations above thresholds of concern for model organisms. We did find evidence of a bias toward downregulation of some genes in animals with higher [THg].
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| Overall design |
Steller sea lion pups were captured on 2 rookery islands in the WDPS (Agattu Island/Gillon Point, and Ulak Island/Hasgox Point) during June 24 - July 17, 2013 and June 18 - July 5, 2015. Blood samples were then collected via the caudal gluteal vein for THg analysis (Vacuette Trace Element, Geiner Labortechnik, Kremsmünter, Austria) and for RNA stabilization and collection (PaxGene? RNA, PreAnalytiX, Hombrechtikon Switzerland). Blood was stored at approximately -15°C for the duration of the cruise (approximately 3 weeks), and placed in a -80°C freezer upon arrival at UAF. RNA-Seq samples were selected from Agattu (n= 18) and Ulak (n=6) Islands, both of which have declining pup counts from 2000 to present (Figure 1b, Fritz et al., 2015). In order to maximize study efficacy while working with limited funding, we decided to analyze samples with high and low [THg] (extremes) rather than treating [THg] as a continuous variable. We selected six individuals with the highest [THg] and lowest [THg] from each year of sampling (2013 and 2015).
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| Contributor(s) |
Harley J, MacDonald JW, Rea L, Bammler TK, Kavanagh T, Fadely B, Gelatt T, O'Hara TM |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
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| Submission date |
Jul 06, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
James William MacDonald |
| E-mail(s) |
jmacdon@uw.edu
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| Organization name |
University of Washington
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| Department |
Environmental and Occupational Health Sciences
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| Street address |
4225 Roosevelt Way NE
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| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98105-6099 |
| Country |
USA |
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| Platforms (2) |
| GPL23666 |
Illumina NextSeq 500 (Eumetopias jubatus) |
| GPL23667 |
Ion Torrent Proton (Eumetopias jubatus) |
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| Samples (13)
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| Relations |
| BioProject |
PRJNA393348 |
| SRA |
SRP111289 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE100883_Raw_counts.txt.gz |
12.8 Mb |
(ftp)(http) |
TXT |
| GSE100883_Trinity.fasta.gz |
153.6 Mb |
(ftp)(http) |
FASTA |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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