Sea Otter Gene Transcription Data from Kodiak, the Alaska Peninsula, and Prince William Sound, Alaska, 2005-2012

Identification_Information:

Citation:

Citation_Information:

Originator: Lizabeth Bowen
Originator: Brenda Ballachey
Originator: James Bodkin
Originator: A. Keith Miles
Originator: Daniel Esler
Originator: Kimberly Kloecker
Publication_Date: 2017
Title:

Geospatial_Data_Presentation_Form: tabular digital data
Publication_Information:

Publication_Place: Anchorage, Alaska
Publisher: U.S. Geological Survey

Other_Citation_Details:

Suggested Citation: Bowen, L., Ballachey, B.E., Bodkin, J.L., Miles, A. K., Esler D. and Kloecker, K. A., 2017, Sea Otter Gene Transcription Data from Kodiak, the Alaska Peninsula and Prince William Sound, Alaska, 2005-2012: U.S. Geological Survey data release, https://doi.org/10.5066/F789141P.

Online_Linkage: https://doi.org/10.5066/F789141P
Larger_Work_Citation:

Citation_Information:

Originator: Lizabeth Bowen
Originator: A. Keith Miles
Originator: Brenda Ballachey
Originator: Shannon Waters
Originator: James Bodkin
Publication_Date: 20160601
Title:

Gene Transcript Profiling in Sea Otters Post-Exxon Valdez Oil Spill: A Tool for Marine Ecosystem Health Assessment

Geospatial_Data_Presentation_Form: journal article
Publication_Information:

Publication_Place: Basel, Switzerland
Publisher: MDPI (Multidisciplinary Digital Publishing Institute)

Online_Linkage: https://doi.org/10.3390/jmse4020039

Description:

Abstract:

This data set includes capture location, date, sex, and results of molecular gene transcription analysis for sea otters (Enhydra lutris) sampled in western Prince William Sound (WPWS), Alaska and comparison samples collected from Kodiak and the Alaska Peninsula, and reference samples collected from captive animals. Samples were collected between 2005 and 2012.

(Molecular gene transcription is the process by which information from the DNA template of a particular gene is transcribed into messenger RNA (mRNA) and eventually translated into a functional protein. The amount of mRNA transcribed from a particular gene is physiologically dictated. Altered levels of gene transcripts provide observable signs of health impairment.)

Purpose:

These data are part of a body of work evaluating spatial and temporal variation in molecular gene transcription as an indicator of exposure of sea otters to residual oil from the 1989 Exxon Valdez Oil Spill (EVOS).

The sea otter biomarker project is a component of the integrated Long-term Monitoring of Marine Conditions and Injured Resources and Services submitted by McCammon et al. in spring 2011 to the Exxon Valdez Oil Spill Trustees Council (EVOSTC). Sea otter populations in Prince William Sound (PWS) were injured as a result of the Exxon Valdez oil spill, with evidence for both immediate acute mortality and longer term injury from chronic exposure to oil spilled in 1989. It appears that full recovery was still not complete as of 2011. Prior EVOSTC projects have examined continuing exposure to lingering oil as a factor constraining recovery, using biomarker assays (gene transcription assays to evaluate exposure and health of sea otters). For sea otters, recent studies have shown that abundance in the vicinity of northern Knight Island has not yet returned to pre-spill levels, and that otters are foraging in areas where lingering oil persists in sediments. Most recently, gene transcription assays have been developed, using an array of genes to specifically quantify oil exposure and health status of sea otters.

Time_Period_of_Content:

Time_Period_Information:

Range_of_Dates/Times:

Beginning_Date: 2005
Ending_Date: 2012

Currentness_Reference: ground condition

Status:

Progress: Complete
Maintenance_and_Update_Frequency: Not planned

Spatial_Domain:

Description_of_Geographic_Extent:

Wild-caught sea otter samples were collected from Knight and Montague Islands in western Prince William Sound, Adak Island in the Aleutian Island archipelago, portions of the Alaska Peninsula along the Katmai National Park and Preserve coast, and in the waters surrounding Kodiak Island, Alaska.

Bounding_Coordinates:

West_Bounding_Coordinate: -177.0996
East_Bounding_Coordinate: -146.777
North_Bounding_Coordinate: 60.695
South_Bounding_Coordinate: 51.344

Keywords:

Theme:

Theme_Keyword_Thesaurus: USGS Metadata Identifier
Theme_Keyword: USGS:ASC118

Theme:

Theme_Keyword_Thesaurus: ISO 19115 Topic Category
Theme_Keyword: Biota
Theme_Keyword: Environment

Theme:

Theme_Keyword_Thesaurus: None
Theme_Keyword: oil exposure
Theme_Keyword: sea otters
Theme_Keyword: Enhydra lutris
Theme_Keyword: gene transcription
Theme_Keyword: biomarker
Theme_Keyword: population recovery
Theme_Keyword: Exxon Valdez Oil Spill
Theme_Keyword: EVOS
Theme_Keyword: ecosystem monitoring

Place:

Place_Keyword_Thesaurus: Geographic Names Information System
Place_Keyword: Prince William Sound
Place_Keyword: Alaska
Place_Keyword: Kodiak Island
Place_Keyword: Adak Island
Place_Keyword: Knight Island
Place_Keyword: Montague Island
Place_Keyword: Katmai National Park and Preserve
Place_Keyword: Alaska Peninsula

Taxonomy:

Keywords/Taxon:

Taxonomic_Keyword_Thesaurus: USGS Biocomplexity Thesaurus
Taxonomic_Keywords: Mammals

Taxonomic_System:

Classification_System/Authority:

Classification_System_Citation:

Citation_Information:

Originator: Integrated Taxonomic Information System
Publication_Date: Unknown
Title: Integrated Taxonomic Information System
Geospatial_Data_Presentation_Form: database
Publication_Information:

Publication_Place: Unknown
Publisher: Integrated Taxonomic Information System

Online_Linkage: http://www.itis.gov

Taxonomic_Procedures: visual identification in the field
Taxonomic_Completeness: not applicable (NA)

General_Taxonomic_Coverage: Data is from samples collected from sea otters, Enhydra lutris
Taxonomic_Classification:

Taxon_Rank_Name: Kingdom
Taxon_Rank_Value: Animalia
Taxonomic_Classification:

Taxon_Rank_Name: Subkingdom
Taxon_Rank_Value: Bilateria
Taxonomic_Classification:

Taxon_Rank_Name: Infrakingdom
Taxon_Rank_Value: Deuterostomia
Taxonomic_Classification:

Taxon_Rank_Name: Phylum
Taxon_Rank_Value: Chordata
Taxonomic_Classification:

Taxon_Rank_Name: Subphylum
Taxon_Rank_Value: Vertebrata
Taxonomic_Classification:

Taxon_Rank_Name: Infraphylum
Taxon_Rank_Value: Gnathostomata
Taxonomic_Classification:

Taxon_Rank_Name: Superclass
Taxon_Rank_Value: Tetrapoda
Taxonomic_Classification:

Taxon_Rank_Name: Class
Taxon_Rank_Value: Mammalia
Taxonomic_Classification:

Taxon_Rank_Name: Subclass
Taxon_Rank_Value: Theria
Taxonomic_Classification:

Taxon_Rank_Name: Infraclass
Taxon_Rank_Value: Eutheria
Taxonomic_Classification:

Taxon_Rank_Name: Order
Taxon_Rank_Value: Carnivora
Taxonomic_Classification:

Taxon_Rank_Name: Suborder
Taxon_Rank_Value: Caniformia
Taxonomic_Classification:

Taxon_Rank_Name: Family
Taxon_Rank_Value: Mustelidae
Taxonomic_Classification:

Taxon_Rank_Name: Subfamily
Taxon_Rank_Value: Lutrinae
Taxonomic_Classification:

Taxon_Rank_Name: Genus
Taxon_Rank_Value: Enhydra
Taxonomic_Classification:

Taxon_Rank_Name: Species
Taxon_Rank_Value: Enhydra lutris
Applicable_Common_Name: Sea Otter
Applicable_Common_Name: Nutria marina
Taxonomic_Classification:

Taxon_Rank_Name: Subspecies
Taxon_Rank_Value: Enhydra lutris kenyoni

Taxonomic_Classification:

Taxon_Rank_Name: Subspecies
Taxon_Rank_Value: Enhydra lutris nereis

Access_Constraints: none
Use_Constraints:

Unless otherwise stated, all data, metadata and related materials are considered to satisfy the quality standards relative to the purpose for which the data were collected. Although these data and associated metadata have been reviewed for accuracy and completeness and approved for release by the U.S. Geological Survey (USGS), no warranty expressed or implied is made regarding the display or utility of the data on any other system or for general or scientific purposes, nor shall the act of distribution constitute any such warranty.

Any use of trade, firm, or product names is for descriptive purposes only and does not imply endorsement by the U.S. Government.

Any person using the information here should fully understand the data collection procedures before beginning analyses. The burden for determining fitness of use lies entirely with the user.

For purposes of publication of dissemination, citations or credit should be given to the authors and USGS.

USGS grants to the public a non-exclusive, royalty-free license to use these data for non-commercial educational or scientific research purposes.

Please let owner know when data are used and cite primary authors and database when using or publishing these data.

This material is based upon work funded by the Exxon Valdez Oil Spill Trustee Council under Project/Program No. 12120114-QR. Any opinions, findings, conclusions, or recommendations expressed herein are those of the author(s) and do not necessarily reflect the views or positions of the Trustee Council.

Point_of_Contact:

Contact_Information:

Contact_Person_Primary:

Contact_Person: Lizabeth Bowen
Contact_Organization: U. S. Geological Survey, Western Ecological Research Center

Contact_Address:

Address_Type: mailing and physical
Address:

Davis Field Station, One Shields Ave., University of California, Davis

City: Davis
State_or_Province: CA
Postal_Code: 95616-5224
Country: United States

Contact_Voice_Telephone: (530) 752-5365
Contact_Electronic_Mail_Address: lbowen@usgs.gov

Data_Set_Credit:

This research was funded in part by the Exxon Valdez Oil Spill Trustee Council. Funding was also provided by the U.S. Geological Survey (USGS) Western Ecological Research Center and the USGS Alaska Science Center. We gratefully acknowledge the assistance of Heather Coletti, George Esslinger, Kim Kloecker, Daniel Monson, Ben Weitzman and Joe Tomoleoni, USGS, and Michael Murray and Marissa Viens, Monterey Bay Aquarium, for sample collections. We thank Robin Keister for laboratory assistance. Samples were collected under permits authorized by the U.S. Fish and Wildlife Service and the approval of the Animal Care and Use Committee of the USGS Alaska Science Center.

Native_Data_Set_Environment:

The original data are stored as an Excel spreadsheet in a Windows operating environment, but have been exported as a comma separated text file for dissemination.

Cross_Reference:

Citation_Information:

Originator:

Esler, D., B.E. Ballachey, L. Bowen, A.K. Miles, R.D. Dickson, and J.D. Henderson

Publication_Date: 2016
Title:

Cessation of oil exposure in harlequin ducks after the Exxon Valdez oil spill: cytochrome P4501A biomarker evidence

Geospatial_Data_Presentation_Form: journal article
Publication_Information:

Publication_Place: NJ
Publisher:

John Wiley & Sons, Inc., Wiley Online Library, Environmental Toxicology and Chemistry

Online_Linkage: https://doi.org/10.1002/etc.3659

Data_Quality_Information:

Attribute_Accuracy:

Attribute_Accuracy_Report:

The following attributes are assumed to be accurate based on laboratory standard techniques: AHR, CaM, CCR3, COX2, CYT, DRB, HDC, HSP70, 5HTT, IL10, IL18, Mx1, and THRB (see Entity/Attribute section for definition of these terms). All samples are run in duplicate. If duplicate values are greater than or equal to 1 Ct value apart, then that sample is rerun. In a situation where there is very little or undetectable transcription, we look at the Ct values of the housekeeping gene (S9) and the RNA concentration to ensure it is within the normal range for that species (based on all the animals we have run). If the RNA concentration is an issue we omit that sample.

Logical_Consistency_Report:

The gene transcription data values reported are normalized Ct values. These are the Ct value of the housekeeping gene (S9) subtracted from the Ct value of the gene of interest. This is the standard format for reporting gene transcription data.

A value of 24 indicates that the Ct value of the housekeeping gene is beyond the detection limits of the technology (i.e., not enough mRNA to measure).

Negative number indicate higher transcription: -4 is a "higher" value than -2 or 2 or 5.

Completeness_Report:

A value of NA indicates missing data.

We developed the last three genes (CaM, CCR3, 5HTT) years after we had analyzed Kodiak. We felt it would be inaccurate to have some genes run on fresh samples and some genes run years later on archived samples so we did not add those extra genes for the Kodiak samples.

Positional_Accuracy:

Horizontal_Positional_Accuracy:

Horizontal_Positional_Accuracy_Report: No formal positional accuracy tests were conducted

Lineage:

Methodology:

Methodology_Type: field
Methodology_Description:

Sea otters were captured and samples and measurements collected.

Methodology_Citation:

Citation_Information:

Originator:

Miles, A.K.; Bowen, L.; Ballachey, B.E.; Bodkin, J.L.; Murray, M.; Estes, J.L.; Keister, R.A.; Stott, J.L.

Publication_Date: 2012
Title:

Variation in transcript profiles in sea otters (Enhydra lutris) from Prince William Sound, Alaska and clinically normal reference otters.

Geospatial_Data_Presentation_Form: document
Online_Linkage: https://doi.org/10.3354/meps09572

Methodology_Citation:

Citation_Information:

Originator:

Bodkin, J.L.; Ballachey, B.E.; Coletti, H.A.; Esslinger, G.G.; Kloecker, K.A.; Rice, S.D.; Reed, J.A.; Monson, D.H.

Publication_Date: 2012
Title:

Long-term effects of the Exxon Valdez oil spill—Sea otter foraging in the intertidal as a pathway of exposure to lingering oil.

Geospatial_Data_Presentation_Form: document
Online_Linkage: https://doi.org/10.3354/meps09523

Methodology:

Methodology_Type: both
Methodology_Description:

A 2.5 mL blood sample from each sea otter was drawn directly into a PAXgene™ blood RNA collection tube (PreAnalytiX©, Switzerland) from either the jugular or popliteal vein and then frozen at – 20degrees C until extraction of RNA. The RNA from blood in PAXgene™ tubes was isolated according to manufacturer’s standard protocols and frozen at - 80 degrees C.

Methodology_Citation:

Citation_Information:

Originator:

Bowen, L, AK Miles, M Murray, H Haulena, J Tuttle, W Van Bonn, L Adams, JL Bodkin, BE Ballachey, MT Tinker, R Keister, and JL Stott.

Publication_Date: 2011
Title:

Gene transcription in sea otters (Enhydra lutris): development of a diagnostic tool for sea otter and ecosystem health.

Geospatial_Data_Presentation_Form: document
Online_Linkage: https://doi.org/10.1111/j.1755-0998.2011.03060.x

Methodology_Citation:

Citation_Information:

Originator:

Bowen, L., Riva, F., Mohr, C., Aldridge, B., Schwartz, J., Miles, A. K., and Stott, J.L.

Publication_Date: 2007
Title:

Differential gene transcription induced by exposure of captive mink to fuel oil: A model for the sea otter.

Geospatial_Data_Presentation_Form: document
Online_Linkage: https://doi.org/10.1007/s10393-007-0113-5

Methodology:

Methodology_Type: Both
Methodology_Description:

All RNA was checked for quality by running on both an agarose gel and on a Nanodrop 2000 and achieved A260/A280 ratios of approximately 2.0 and A260/A230 ratios of less than 1.0. A standard cDNA synthesis was performed on 2 μg of mRNA template from each animal. Quantitative real-time polymerase chain reaction (qPCR) systems for the individual, sea otter-specific housekeeping gene (S9) and genes of interest were run in separate wells. Amplifications were conducted on a 7300 Real-time Thermal Cycler (Applied Biosystems™, Foster City, Calif.) with reaction conditions identical to those in Bowen et al. (2007, 2011) and Miles et al. (2012).

Methodology_Citation:

Citation_Information:

Originator:

Miles, A.K.; Bowen, L.; Ballachey, B.E.; Bodkin, J.L.; Murray, M.; Estes, J.L.; Keister, R.A.; Stott, J.L.

Publication_Date: 2012
Title:

Variation in transcript profiles in sea otters (Enhydra lutris) from Prince William Sound, Alaska and clinically normal reference otters.

Geospatial_Data_Presentation_Form: document
Online_Linkage: https://doi.org/10.3354/meps09572

Methodology_Citation:

Citation_Information:

Originator:

Bowen, L., Riva, F., Mohr, C., Aldridge, B., Schwartz, J., Miles, A. K., and Stott, J.L.

Publication_Date: 2007
Title:

Differential gene transcription induced by exposure of captive mink to fuel oil: A model for the sea otter.

Geospatial_Data_Presentation_Form: document
Online_Linkage: https://doi.org/10.1007/s10393-007-0113-5

Methodology_Citation:

Citation_Information:

Originator:

Bowen, L, AK Miles, M Murray, H Haulena, J Tuttle, W Van Bonn, L Adams, JL Bodkin, BE Ballachey, MT Tinker, R Keister, and JL Stott.

Publication_Date: 2011
Title:

Gene transcription in sea otters (Enhydra lutris): development of a diagnostic tool for sea otter and ecosystem health.

Geospatial_Data_Presentation_Form: document
Online_Linkage: https://doi.org/10.1111/j.1755-0998.2011.03060.x

Process_Step:

Process_Description:

Field data were entered on hard copy data sheets. At the end of each field trip, data were entered into an excel spreadsheet.

Process_Date: Unknown

Process_Step:

Process_Description:

Results from laboratory analyses were added to the spreadsheets with the field data.

Process_Date: Unknown

Spatial_Data_Organization_Information:

Indirect_Spatial_Reference: Geographic Names Index System (GNIS)
Direct_Spatial_Reference_Method: Point

Entity_and_Attribute_Information:

Detailed_Description:

Entity_Type:

Entity_Type_Label: Sea otter gene transcription values, Alaska 2005-2012
Entity_Type_Definition: spreadsheet
Entity_Type_Definition_Source: producer defined

Attribute:

Attribute_Label: Date Capture
Attribute_Definition:

Date of capture of sea otter. Most are M/D/Y except the Kodiak captures which only have a year listed.

Attribute_Definition_Source: producer defined
Attribute_Domain_Values:

Range_Domain:

Range_Domain_Minimum: 2005
Range_Domain_Maximum: 8/22/2012
Attribute_Units_of_Measure: calendar date

Attribute:

Attribute_Label: Location
Attribute_Definition: Broad, inconsistent, description of where otter was captured.
Attribute_Definition_Source: producer defined
Attribute_Domain_Values:

Enumerated_Domain:

Enumerated_Domain_Value: Alaska
Enumerated_Domain_Value_Definition: Otter captured and sampled in Alaska
Enumerated_Domain_Value_Definition_Source: producer defined

Attribute_Domain_Values:

Enumerated_Domain:

Enumerated_Domain_Value: Alaska Peninsula
Enumerated_Domain_Value_Definition: Otter captured and sampled in waters of the Alaska Peninsula
Enumerated_Domain_Value_Definition_Source: producer defined

Attribute_Domain_Values:

Enumerated_Domain:

Enumerated_Domain_Value: Aleutian
Enumerated_Domain_Value_Definition: Otter captured and sampled in the western Aleutian Islands
Enumerated_Domain_Value_Definition_Source: producer defined

Attribute_Domain_Values:

Enumerated_Domain:

Enumerated_Domain_Value: Captive
Enumerated_Domain_Value_Definition: Otter housed in a zoo or aquarium and sampled there
Enumerated_Domain_Value_Definition_Source: producer defined

Attribute_Domain_Values:

Enumerated_Domain:

Enumerated_Domain_Value: Katmai
Enumerated_Domain_Value_Definition:

Otter captured and sampled from the Katmai National Park and Preserve coast

Enumerated_Domain_Value_Definition_Source: producer defined

Attribute_Domain_Values:

Enumerated_Domain:

Enumerated_Domain_Value: Western Prince William Sound
Enumerated_Domain_Value_Definition:

Otter captured and sampled in western Prince William Sound, specifically in an area impacted by the 1989 Exxon Valdez Oil Spill

Enumerated_Domain_Value_Definition_Source: producer defined

Attribute:

Attribute_Label: Specific Location
Attribute_Definition:

Text description or name of more specific capture location where location is named

Attribute_Definition_Source: producer defined
Attribute_Domain_Values:

Unrepresentable_Domain:

In most cases a more specific location of where an otter was captured and sampled. 'NA' is used for captive otters.

Attribute:

Attribute_Label: Sample ID
Attribute_Definition:

Identifying code for individual sea otters. Captive otters may have names or codes. Wild-caught otters have a combination of capture year and sequential numbering and sometimes location. Since individual otters can be recaptured in different years, Sample ID alone may not be a unique identifier. In some cases the original sea otter ID code was appended with the additional capture year to make Sample ID unique.

Attribute_Definition_Source: producer defined
Attribute_Domain_Values:

Unrepresentable_Domain:

Sample ID is in most cases the otter ID code, for example KOD 05 001 is the first otter sampled at Kodiak in 2005. Since otters can be captured in more than one year, the year a sample was collected for this analysis was appended to the otter code to create the Sample ID, for example SO-08-31 and SO-08-31-10 are both samples from the 31st otter captured in 2008, but the latter sample was from when that otter was recaptured in 2010. Sample ID may be a name or code for captive animals.

Attribute:

Attribute_Label: SEX
Attribute_Definition: sex of sampled sea otter
Attribute_Definition_Source: producer defined
Attribute_Domain_Values:

Enumerated_Domain:

Enumerated_Domain_Value: F
Enumerated_Domain_Value_Definition: Female
Enumerated_Domain_Value_Definition_Source: producer defined

Attribute_Domain_Values:

Enumerated_Domain:

Enumerated_Domain_Value: M
Enumerated_Domain_Value_Definition: Male
Enumerated_Domain_Value_Definition_Source: producer defined

Attribute:

Attribute_Label: AHR
Attribute_Definition:

The arylhydrocarbon receptor (AHR gene) responds to classes of environmental toxicants including polycyclic aromatic hydrocarbons (PAHs), polyhalogenated hydrocarbons, dibenzofurans, and dioxin. Depending upon the ligand, AHR signaling can modulate T-regulatory (TREG) (immune-suppressive) or T-helper type 17 (TH17) (pro-inflammatory) immunologic activity. Values presented are normalized by subtracting the Ct of the housekeeping gene from the Ct of the gene of interest.

Attribute_Definition_Source: producer defined
Attribute_Domain_Values:

Range_Domain:

Range_Domain_Minimum: 5.65
Range_Domain_Maximum: 24
Attribute_Units_of_Measure: Cycle threshold transcription value (Ct)

Attribute:

Attribute_Label: CaM
Attribute_Definition:

Calmodulin (CaM) is a small acidic Ca2+-binding protein, with a structure and function that is highly conserved in all eukaryotes. CaM activates various Ca2+-dependent enzyme reactions, thereby modulating a wide range of cellular events, including metabolism control, muscle contraction, exocytosis of hormones and neurotransmitters, and cell division and differentiation. Values presented are normalized by subtracting the CT of the housekeeping gene from the CT of the gene of interest. NA indicates 'not applicable' when there are no data from Kodiak samples. See note in completeness report section of metadata.