DNA microsatellite markers for Mustard Hill Coral (Porites astreoides) from the Florida Keys Reef Tract

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Metadata:

Identification_Information:
Citation:
Citation_Information:
Originator: Gallery, Dominique N.
Originator: Kuffner, Ilsa B.
Originator: Toth, Lauren T.
Publication_Date: 20210430
Title:
DNA microsatellite markers for Mustard Hill Coral (Porites astreoides) from the Florida Keys Reef Tract
Geospatial_Data_Presentation_Form: tabular digital data
Larger_Work_Citation:
Citation_Information:
Originator: Gallery, Dominique N.
Originator: Kuffner, Ilsa B.
Originator: Toth, Lauren T.
Publication_Date: 20210430
Title:
DNA microsatellite markers for Mustard Hill Coral (Porites astreoides) from the Florida Keys Reef Tract
Series_Information:
Series_Name: U.S. Geological Survey data release
Issue_Identification: doi:10.5066/P9R8NZ2J
Publication_Information:
Publication_Place: St. Petersburg, Florida
Publisher:
U.S. Geological Survey - St. Petersburg Coastal and Marine Science Center
Online_Linkage: https://doi.org/10.5066/P9R8NZ2J
Description:
Abstract:
This data set includes: (1) allele sizes of 11 previously published microsatellites (Kenkel and others, 2013; Shearer and Coffroth, 2004) for 39 individuals of mustard hill coral, Porites astreoides (mustard hill coralP. astreoides) collected in the Spring of 2017 from four locations in the Florida Keys Reef Tract (FKRT): Fowey Rocks, Crocker Reef, Sombrero Reef and Pulaski Shoal and (2) the deoxyribonucleic acid (DNA) concentration of the extracted DNA prior to polymerase chain reaction (PCR) reactions for the samples. These data were used in Gallery and others (2021) to evaluate the genetic diversity and connectivity of individuals among and between sites.
Purpose:
Microsatellites were used to determine the genetic relatedness of the sampled Porites astreoides in the Florida Keys.
Time_Period_of_Content:
Time_Period_Information:
Multiple_Dates/Times:
Single_Date/Time:
Calendar_Date: 201705
Single_Date/Time:
Calendar_Date: 201909
Single_Date/Time:
Calendar_Date: 201908
Single_Date/Time:
Calendar_Date: 201911
Currentness_Reference: Date of process steps
Status:
Progress: Complete
Maintenance_and_Update_Frequency: None planned
Spatial_Domain:
Bounding_Coordinates:
West_Bounding_Coordinate: -82.77280
East_Bounding_Coordinate: -80.09560
North_Bounding_Coordinate: 25.59047
South_Bounding_Coordinate: 24.62687
Keywords:
Theme:
Theme_Keyword_Thesaurus: USGS Metadata Identifier
Theme_Keyword: USGS:99036c02-ead0-4f81-aa00-cc32f825f223
Theme:
Theme_Keyword_Thesaurus: USGS Thesaurus
Theme_Keyword: marine biology
Theme_Keyword: genetic diversity
Theme_Keyword: genotype
Theme_Keyword: population and community ecology
Theme_Keyword: population dynamics
Theme_Keyword: molecular biology
Theme_Keyword: coelenterates
Place:
Place_Keyword_Thesaurus: None
Place_Keyword: Florida Keys
Place_Keyword: Pulaski Shoal
Place_Keyword: Sombrero Reef
Place_Keyword: Crocker Reef
Place_Keyword: Fowey Rocks
Access_Constraints: none
Use_Constraints: none
Point_of_Contact:
Contact_Information:
Contact_Person_Primary:
Contact_Person: Lauren T. Toth
Contact_Organization:
U.S. Geological Survey, St. Petersburg Coastal and Marine Science Center
Contact_Position: Physical Scientist
Contact_Address:
Address_Type: mailing and physical
Address: 600 4Th Street South
City: St. Petersburg
State_or_Province: Florida
Postal_Code: 33701
Country: United States
Contact_Voice_Telephone: 727-502-8029
Contact_Electronic_Mail_Address: ltoth@usgs.gov
Cross_Reference:
Citation_Information:
Originator: D.N. Gallery
Originator: M.L. Green
Originator: I.B. Kuffner
Originator: E.A. Lenz
Originator: L.T. Toth
Publication_Date: 20210709
Title:
Genetic structure and diversity of the mustard hill coral Porites astreoides along the Florida Keys reef tract
Publication_Information:
Publication_Place: Berlin, Germany
Publisher: Marine Biodiversity, Springer Nature
Online_Linkage: https://doi.org/10.1007/s12526-021-01196-7
Cross_Reference:
Citation_Information:
Originator: C.D. Kenkel
Originator: G. Goodbody-Gringley
Originator: D. Caillaud
Originator: S.W. Davies
Originator: E. Bartels
Originator: M.V. Matz
Publication_Date: 20130730
Title:
Evidence for a host role in thermotolerance divergence between populations of the mustard hill coral (Porites astreoides) from different reef environments
Publication_Information:
Publication_Place: Hoboken, New Jersey
Publisher: Molecular Ecology, Wiley
Online_Linkage: https://doi.org/10.1111/mec.12391
Cross_Reference:
Citation_Information:
Originator: T.L. Shearer
Originator: M.A. Coffroth
Publication_Date: 20040608
Title:
Isolation of microsatellite loci from the scleractinian corals, Montastraea cavernosa and Porites astreoides
Publication_Information:
Publication_Place: Hoboken, New Jersey
Publisher: Molecular Ecology Notes, Wiley
Online_Linkage: https://doi.org/10.1111/j.1471-8286.2004.00653.x
Cross_Reference:
Citation_Information:
Originator: C. van Oosterhout
Originator: W.F. Hutchinson
Originator: D.P.M. Wills
Originator: P. Shipley
Publication_Date: 20040608
Title:
Micro-Checker: software for identifying and correcting genotyping errors in microsatellite data
Publication_Information:
Publication_Place: Hoboken, New Jersey
Publisher: Molecular Ecology Notes, Wiley
Online_Linkage: https://doi.org/10.1111/j.1471-8286.2004.00684.x
Cross_Reference:
Citation_Information:
Originator: S.W. Davies
Originator: M. Rahman
Originator: E. Meyer
Originator: E.A. Green
Originator: E. Buschiazzo
Originator: M. Medina
Originator: M.V. Matz
Publication_Date: 20121031
Title:
Novel polymorphic microsatellite markers for population genetics of the endangered Caribbean star coral, Montastraea faveolata
Publication_Information:
Publication_Place: Berlin, Germany
Publisher: Marine Biodiversity, Springer
Online_Linkage: https://doi.org/10.1007/s12526-012-0133-4
Cross_Reference:
Citation_Information:
Originator: A. Baker
Originator: R. Cunning
Publication_Date: 20160304
Title: Bulk gDNA extraction from coral samples
Publication_Information:
Publication_Place: Online
Publisher: protocols.io
Online_Linkage: https://doi.org/10.17504/protocols.io.dyq7vv
Cross_Reference:
Citation_Information:
Originator: I.B. Kuffner
Originator: T.D. Hickey
Originator: J.M. Morrison
Publication_Date: 20130608
Title:
Calcification rates of the massive coral Siderastrea siderea and crustose coralline algae along the Florida Keys (USA) outer-reef tract
Publication_Information:
Publication_Place: Berlin, Germany
Publisher: Coral Reefs, Springer
Online_Linkage: https://doi.org/10.1007/s00338-013-1047-8
Cross_Reference:
Citation_Information:
Originator: J.M. Morrison
Originator: I.B. Kuffner
Originator: T.D. Hickey
Publication_Date: 20130730
Title:
Methods for monitoring corals and crustose coralline algae to quantify in-situ calcification rates
Publication_Information:
Publication_Place: Reston, VA
Publisher: U.S. Geological Survey
Online_Linkage: http://pubs.usgs.gov/of/2013/1159/
Cross_Reference:
Citation_Information:
Originator: E.A. Lenz
Originator: L.A. Bartlett
Originator: A. Stathakopoulos
Originator: I.B. Kuffner
Publication_Date: 20210622
Title:
Physiological differences in bleaching response of the coral Porites astreoides along the Florida Keys reef tract during high-temperature stress
Publication_Information:
Publication_Place: Lausanne, Switzerland
Publisher: Frontiers in Marine Science, Frontiers
Online_Linkage: https://doi.org/10.3389/fmars.2021.615795
Data_Quality_Information:
Attribute_Accuracy:
Attribute_Accuracy_Report:
Individual sample ID's were cross-checked and verified in Microsoft Excel Version 2002 worksheets for extraction, PCR, and placement into plates sent for data analysis. For quality control, all samples were run on an agarose gel to ensure DNA extraction was successful prior to running PCR. Microsatellite marker calls were processed through Micro-Checker V. 2.2.3 (van Oosterhout and others 2004) to detect errors in data interpretation.
Logical_Consistency_Report:
Reported allele sizes were reviewed to confirm they conform to expected distributions using Micro-Checker V. 2.2.3 (van Oosterhout and others 2004).
Completeness_Report:
Any data omissions for entities are explained in the Entity and Attribute definition section below. Blank data indicates data was homozygous for that allele. Attribute data equaling “NP” in a cell of the data set refers to a sample that did not amplify or show any product (“no product”). Attribute data equaling "?" refers to a sample with product not sufficient (DNA concentration too low) to call the allele.
Positional_Accuracy:
Horizontal_Positional_Accuracy:
Horizontal_Positional_Accuracy_Report: No formal positional accuracy tests were conducted
Vertical_Positional_Accuracy:
Vertical_Positional_Accuracy_Report: No formal positional accuracy tests were conducted
Lineage:
Process_Step:
Process_Description:
Porites astreoides samples were obtained from four locations along the FKRT using a Global Positioning System (GPS): Fowey Rocks in Biscayne National Park (25.59047, -80.09560), Crocker Reef in the Upper Florida Keys (24.90908, -80.52665), Sombrero Reef in the Middle Florida Keys (24.62687, -81.10893), and Pulaski Shoal in the Dry Tortugas National Park (24.69355, -82.77280). The corals were collected within a 100 to 200 square meter area at each site, and colonies selected for sampling were no closer than approximately 20 meters (Lenz and others, 2021; compare with Kuffner and others, 2013). After collection, the corals were grown for two years (from 2015 to 2017) on cinderblocks installed on the reef as part of the U.S. Geological Survey calcification assessment project (Kuffner and others 2013; Morrison and others 2013). Coral colony condition was assessed, and growth rates were monitored every six months during the study using the methods outlined in Kuffner and others (2013; data presented in Lenz and others, 2021). At the end of the two-year period, several 4 millimeter thick slabs were cut from the center of the colonies. One slab was used for host tissue sampling in this study as well as symbiont sampling and histological examination in an associated study (Lenz and others, 2021). The rest of the colonies were outplanted onto the reefs.
Process_Date: 201705
Process_Contact:
Contact_Information:
Contact_Person_Primary:
Contact_Person: Ilsa B.Kuffner
Contact_Organization:
U.S. Geological Survey, St. Petersburg Coastal and Marine Science Center
Contact_Address:
Address_Type: mailing and physical
Address: 600 4th Street South
City: St. Petersburg
State_or_Province: Florida
Postal_Code: 33701
Country: United States
Contact_Voice_Telephone: 727-502-8048
Contact_Electronic_Mail_Address: ikuffner@usgs.gov
Process_Step:
Process_Description:
DNA Extraction: Preparation of cetyltrimethylammonium bromide (CTAB) mixture (Baker and Cunning 2016).
Process_Date: 201905
Process_Contact:
Contact_Information:
Contact_Person_Primary:
Contact_Person: Dominique N. Gallery
Contact_Organization:
University of South Florida, U.S. Geological Survey, St. Petersburg Coastal and Marine Science Center
Contact_Address:
Address_Type: mailing and physical
Address: 600 4th Street South
City: St. Petersburg
State_or_Province: Florida
Postal_Code: 33701
Country: United States
Contact_Voice_Telephone: 727-502-8000
Contact_Electronic_Mail_Address: dgallery@mail.usf.edu
Process_Step:
Process_Description: Quibit 3.0 analysis to quantify DNA extracted.
Process_Date: 201905
Process_Contact:
Contact_Information:
Contact_Person_Primary:
Contact_Person: Dominique N. Gallery
Contact_Organization:
University of South Florida, U.S. Geological Survey, St. Petersburg Coastal and Marine Science Center
Contact_Address:
Address_Type: mailing and physical
Address: 600 4th Street South
City: St. Petersburg
State_or_Province: Florida
Postal_Code: 33701
Country: United States
Contact_Voice_Telephone: 727-502-8000
Contact_Electronic_Mail_Address: dgallery@mail.usf.edu
Process_Step:
Process_Description:
Run electrophoresis gel using a 1.5% agarose gel suspension to visualize DNA extraction.
Process_Date: 201905
Process_Contact:
Contact_Information:
Contact_Person_Primary:
Contact_Person: Dominique N. Gallery
Contact_Organization:
University of South Florida, U.S. Geological Survey, St. Petersburg Coastal and Marine Science Center
Contact_Address:
Address_Type: mailing and physical
Address: 600 4th Street South
City: St. Petersburg
State_or_Province: Florida
Postal_Code: 33701
Country: United States
Contact_Voice_Telephone: 727-502-8000
Contact_Electronic_Mail_Address: dgallery@mail.usf.edu
Process_Step:
Process_Description:
Amplified DNA using PCR in 10 microliter (μL) reactions with 10 nanograms (ng) DNA, 1 micromole (μM) fluorescently-labeled forward primer, 1 μM reverse primer, 0.2 millimole (mM) deoxynucleoside triphosphate (dNTP) (Promega), 2μL 5 times (5x) PCR GoTaq Flexi buffer (Promega), 0.25 units (0.05 μL) GoTaq Flexi polymerase (Promega), 2 mM MgCl2 (Promega). The PCR procedure was based on the protocols of Davies and others (2013), but was modified as follows: (1) increased to 1 μM fluorescently-labeled forward primer and 1 μM reverse primer, (2) modified to 2 μL 5X PCR GoTaq Flexi buffer (Promega). Increased 0.25 U GoTaq Flexi polymerase (Promega), (3) added 2 mM magnesium chloride (MgCl2) (Promega), and (4) thermocycler protocol modifications: Increased initial denaturing temperature 95 degrees Celsius (˚C). Increased number of cycles to 40 at (95˚C for 40 seconds, 58–60˚C for 60 seconds, 72˚C for 60 seconds).
Process_Date: 201908
Process_Contact:
Contact_Information:
Contact_Person_Primary:
Contact_Person: Dominique N. Gallery
Contact_Organization:
University of South Florida, U.S. Geological Survey, St. Petersburg Coastal and Marine Science Center
Contact_Address:
Address_Type: mailing and physical
Address: 600 4th Street South
City: St. Petersburg
State_or_Province: Florida
Postal_Code: 33701
Country: United States
Contact_Voice_Telephone: 727-502-8000
Contact_Electronic_Mail_Address: dgallery@mail.usf.edu
Process_Step:
Process_Description:
Sent select samples to the University of Illinois Urbana-Champagne (UIUC) Core Sequencing Facility for fragment analysis of dilution sets to determine optimum dilution for each primer set.
Process_Date: 201908
Process_Contact:
Contact_Information:
Contact_Person_Primary:
Contact_Person: Unknown
Contact_Organization:
University of Illinois Urbana-Champagne Core Sequencing Facility
Contact_Address:
Address_Type: mailing and physical
Address: 334 Edward R. Madigan Laboratory, 1201 W. Gregory Drive
City: Urbana
State_or_Province: Illinois
Postal_Code: 61801
Country: United States
Contact_Voice_Telephone: 217-333-9520
Contact_Electronic_Mail_Address: dna-seq@illinois.edu
Process_Step:
Process_Description:
Sent samples to the UIUC Core Sequencing Facility for fragment analysis using Applied Biosystems 3730x1 DNA Analyzer and ROX1000 standards.
Process_Date: 201909
Process_Contact:
Contact_Information:
Contact_Person_Primary:
Contact_Person: Unknown
Contact_Organization:
University of Illinois Urbana-Champagne Core Sequencing Facility
Contact_Address:
Address_Type: mailing and physical
Address: 334 Edward R. Madigan Laboratory, 1201 W. Gregory Drive
City: Urbana
State_or_Province: Illinois
Postal_Code: 61801
Country: United States
Contact_Voice_Telephone: 217-333-9520
Contact_Electronic_Mail_Address: dna-seq@illinois.edu
Process_Step:
Process_Description:
USGS researchers worked with collaborators at University of South Florida (USF), Saint Petersburg to analyze microsatellites using GeneMapper 5.0 to determine microsatellite calls. Micro-Checker (version 2.2.3) was used to confirm that calls were accurate (for example, correct number of bases between calls). Allele bins were assigned by rounding observed size to the closest integer, except when Micro-Checker indicated that the bins should be adjusted due to errors with nucleotide repeats (for example, only 2 base pairs [bp] difference for trinucleotide repeats). In those cases, alleles were marked as unknown "?" instead of called.
Process_Date: 201910
Process_Contact:
Contact_Information:
Contact_Person_Primary:
Contact_Person: Dominique N. Gallery
Contact_Organization:
University of South Florida, U.S. Geological Survey, St. Petersburg Coastal and Marine Science Center
Contact_Address:
Address_Type: mailing and physical
Address: 600 4th Street South
City: St. Petersburg
State_or_Province: Florida
Postal_Code: 33701
Country: United States
Contact_Voice_Telephone: 727-502-8000
Contact_Electronic_Mail_Address: dgallery@mail.usf.edu
Process_Step:
Process_Description:
Reran PCR for samples that failed to amplify well or indicated potential null alleles.
Process_Date: 201911
Process_Contact:
Contact_Information:
Contact_Person_Primary:
Contact_Person: Dominique N. Gallery
Contact_Organization:
University of South Florida, U.S. Geological Survey, St. Petersburg Coastal and Marine Science Center
Contact_Address:
Address_Type: mailing and physical
Address: 600 4th Street South
City: St. Petersburg
State_or_Province: Florida
Postal_Code: 33701
Country: United States
Contact_Voice_Telephone: 727-502-8000
Contact_Electronic_Mail_Address: dgallery@mail.usf.edu
Process_Step:
Process_Description:
Sent rerun samples to the UIUC Core Sequencing Facility for fragment analysis using Applied Biosystems 3730x1 DNA Analyzer and ROX1000 standards. "GeneScan™ 1000 ROX™ Size Standard is an internal lane size standard developed for use with Applied Biosystems® fluorescence-based DNA electrophoresis systems. The use of an internal lane size standard during electrophoresis enables automated data analysis and precise DNA fragment size comparisons between electrophoresis runs. GeneScan™ 1000 ROX™ Size Standard is designed for sizing DNA fragments in the 47–946 bp range and provides labeled fragments of 47, 51, 55, 82, 85 93 99, 126, 136, 262, 293, 317, 439, 557, 692, 695 and 946 bases. Each of the DNA fragments is labeled with ROX™ fluorophore, which results in a single peak when run under non-denaturing conditions." Quotation is from the ThermoFisher Catalog # 401098
Process_Date: 201911
Process_Contact:
Contact_Information:
Contact_Person_Primary:
Contact_Person: Unknown
Contact_Organization:
University of Illinois Urbana-Champagne Core Sequencing Facility
Contact_Address:
Address_Type: mailing and physical
Address: 334 Edward R. Madigan Laboratory, 1201 W. Gregory Drive
City: Urbana
State_or_Province: Illinois
Postal_Code: 61801
Country: United States
Contact_Voice_Telephone: 217-333-9520
Contact_Electronic_Mail_Address: dna-seq@illinois.edu
Spatial_Data_Organization_Information:
Indirect_Spatial_Reference:
GPS coordinates collected at the four study sites, Fowey Rocks, Crocker Reef, Sombrero Reef, Pulaski Shoal Light
Direct_Spatial_Reference_Method: Point
Spatial_Reference_Information:
Horizontal_Coordinate_System_Definition:
Geographic:
Latitude_Resolution: 0.0197864699
Longitude_Resolution: 0.0228595953
Geographic_Coordinate_Units: Decimal degrees
Geodetic_Model:
Horizontal_Datum_Name: D_WGS_1984
Ellipsoid_Name: WGS_1984
Semi-major_Axis: 6378137.0
Denominator_of_Flattening_Ratio: 298.257223563
Entity_and_Attribute_Information:
Detailed_Description:
Entity_Type:
Entity_Type_Label:
Porites astreoides Microsatellite Data.csv, Porites astreoides Microsatellite Data.xlsx
Entity_Type_Definition:
Microsoft Excel comma-separated values (.csv) and worksheet (.xlsx) files containing data for the Microsatellite markers for Porites astreoides
Entity_Type_Definition_Source: Authors
Attribute:
Attribute_Label: Sample Name
Attribute_Definition:
This is a U.S. Geological Survey, Coastal and Marine Science Center numeric or alphanumeric label that uniquely identifies each sample. Three numbers identify the sample. Negative controls use the identifier "NEG".
Attribute_Definition_Source: USGS
Attribute_Domain_Values:
Unrepresentable_Domain:
A unique identifier given tofor each sample. A three-digit number was given to a tested sample. Negative controls were given the alphanumeric identifier "NEGP#".
Attribute:
Attribute_Label: Sample Type
Attribute_Definition: Identification of sample or negative control.
Attribute_Definition_Source: USGS
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: Sample
Enumerated_Domain_Value_Definition: Sample of P. astreoides
Enumerated_Domain_Value_Definition_Source: USGS
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: Negative Control
Enumerated_Domain_Value_Definition:
Negative controls were utilized to ensure there was no cross-contamination during PCR.
Enumerated_Domain_Value_Definition_Source: USGS
Attribute:
Attribute_Label: Sample Location
Attribute_Definition: The study site at which the sample was collected.
Attribute_Definition_Source: USGS
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: PLS
Enumerated_Domain_Value_Definition: Pulaski Shoal
Enumerated_Domain_Value_Definition_Source: USGS
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: SMK
Enumerated_Domain_Value_Definition: Sombrero Reef
Enumerated_Domain_Value_Definition_Source: USGS
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: FWY
Enumerated_Domain_Value_Definition: Fowey Rocks
Enumerated_Domain_Value_Definition_Source: USGS
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: CRK
Enumerated_Domain_Value_Definition: Crocker Reef
Enumerated_Domain_Value_Definition_Source: USGS
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: Negative
Enumerated_Domain_Value_Definition: Negative control has no location of origin.
Enumerated_Domain_Value_Definition_Source: USGS
Attribute:
Attribute_Label: Panel
Attribute_Definition:
Microsatellite loci used for PCR amplification. Primers that begin with "Past_" are published in Kenkel and others (2013). Primers that begin with "PaGA" are published in Shearer and Coffroth (2004).
Attribute_Definition_Source: USGS
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: Past_2
Enumerated_Domain_Value_Definition: Primer "Past_2" as published in Kenkel and others (2013)
Enumerated_Domain_Value_Definition_Source: Kenkel and others (2013)
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: Past_3
Enumerated_Domain_Value_Definition: Primer "Past_3" as published in Kenkel and others (2013)
Enumerated_Domain_Value_Definition_Source: Kenkel and others (2013)
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: PaGA7
Enumerated_Domain_Value_Definition: Primer "PaGA7" as published in Shearer and Coffroth (2004)
Enumerated_Domain_Value_Definition_Source: Kenkel and others (2013)
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: Past_8
Enumerated_Domain_Value_Definition: Primer "Past_8" as published in Kenkel and others (2013)
Enumerated_Domain_Value_Definition_Source: Kenkel and others (2013)
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: Past_10
Enumerated_Domain_Value_Definition: Primer "Past_10" as published in Kenkel and others (2013)
Enumerated_Domain_Value_Definition_Source: Kenkel and others (2013)
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: Past_13
Enumerated_Domain_Value_Definition: Primer "Past_13" as published in Kenkel and others (2013)
Enumerated_Domain_Value_Definition_Source: Kenkel and others (2013)
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: Past_16
Enumerated_Domain_Value_Definition: Primer "Past_16" as published in Kenkel and others (2013)
Enumerated_Domain_Value_Definition_Source: Kenkel and others (2013)
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: Past_17
Enumerated_Domain_Value_Definition: Primer "Past_17" as published in Kenkel and others (2013)
Enumerated_Domain_Value_Definition_Source: Kenkel and others (2013)
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: Past_21
Enumerated_Domain_Value_Definition: Primer "Past_21" as published in Kenkel and others (2013)
Enumerated_Domain_Value_Definition_Source: Kenkel and others (2013)
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: PaGA24
Enumerated_Domain_Value_Definition: Primer "PaGA24" as published in Shearer and Coffroth (2004)
Enumerated_Domain_Value_Definition_Source: Shearer and Coffroth (2004)
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: PaGA63
Enumerated_Domain_Value_Definition: Primer "PaGA63" as published in Shearer and Coffroth (2004)
Enumerated_Domain_Value_Definition_Source: Shearer and Coffroth (2004)
Attribute:
Attribute_Label: Run Date
Attribute_Definition:
The date the run was processed by UIUC Core Sequencing Facility.
Attribute_Definition_Source: USGS
Attribute_Domain_Values:
Range_Domain:
Range_Domain_Minimum: 08/15/2019
Range_Domain_Maximum: 11/13/2019
Attribute_Units_of_Measure: Dates in MM/DD/YYYY format
Attribute:
Attribute_Label: Allele 1
Attribute_Definition:
The first allele called from Gene-Mapper program. An integer value for called alleles. "NP" indicates there was no product visible in Gene-Mapper to call. "?" indicates there was product visible, but the result was not strong enough to definitively call the allele.
Attribute_Definition_Source: USGS
Attribute_Domain_Values:
Range_Domain:
Range_Domain_Minimum: 139
Range_Domain_Maximum: 463
Attribute_Units_of_Measure: Base pairs
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: NP
Enumerated_Domain_Value_Definition:
NP indicates there was no product visible in Gene-Mapper to call.
Enumerated_Domain_Value_Definition_Source: USGS
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: ?
Enumerated_Domain_Value_Definition:
"?" indicates there was product visible, but the result was not strong enough to definitively call the allele.
Enumerated_Domain_Value_Definition_Source: USGS
Attribute:
Attribute_Label: Allele 2
Attribute_Definition:
The second allele called from Gene-Mapper program. An integer value for called alleles. "NP" indicates there was no product visible in Gene-Mapper to call. "?" indicates there was product visible, but the result was not strong enough to definitively call the allele. Homozygous alleles have the same value from Allele 1 repeated in Allele 2.
Attribute_Definition_Source: USGS
Attribute_Domain_Values:
Range_Domain:
Range_Domain_Minimum: 141
Range_Domain_Maximum: 463
Attribute_Units_of_Measure: Base pairs
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: NP
Enumerated_Domain_Value_Definition: Indicates there was no product visible in Gene-Mapper to call.
Enumerated_Domain_Value_Definition_Source: USGS
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: ?
Enumerated_Domain_Value_Definition:
? indicates there was product visible, but the result was not strong enough to definitively call the allele.
Enumerated_Domain_Value_Definition_Source: USGS
Attribute:
Attribute_Label: Size 1
Attribute_Definition:
A non-integer number that is the exact number of base pairs determined by Gene-Mapper based on Rox1000 dye size standard. NP indicates there was no product visible in Gene-Mapper.
Attribute_Definition_Source: USGS
Attribute_Domain_Values:
Range_Domain:
Range_Domain_Minimum: 139.02
Range_Domain_Maximum: 462.80
Attribute_Units_of_Measure: Base pairs
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: NP
Enumerated_Domain_Value_Definition: Indicates there was no product visible in Gene-Mapper to call.
Enumerated_Domain_Value_Definition_Source: USGS
Attribute:
Attribute_Label: Size 2
Attribute_Definition:
A non-integer number that is the exact number of base pairs determined by Gene-Mapper based on Rox1000 dye size standard. NP indicates there was no product visible in Gene-Mapper. Homozygous alleles have the same value from Size 1 repeated in Size 2
Attribute_Definition_Source: USGS
Attribute_Domain_Values:
Range_Domain:
Range_Domain_Minimum: 141.18
Range_Domain_Maximum: 463.80
Attribute_Units_of_Measure: Base pairs
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: NP
Enumerated_Domain_Value_Definition: NP indicates there was no product visible in Gene-Mapper.
Enumerated_Domain_Value_Definition_Source: USGS
Detailed_Description:
Entity_Type:
Entity_Type_Label:
Porites_astreoides_DNA_concentration.csv, Porites_astreoides_DNA_concentration.xlsx
Entity_Type_Definition:
Microsoft Excel comma-separated values (.csv) and worksheet (.xlsx) files containing data for the concentration of DNA from Porites astreoides samples as determined by Qubit 3.0. These values were used to determine the volume of DNA added to PCR.
Entity_Type_Definition_Source: USGS
Attribute:
Attribute_Label: Run Date
Attribute_Definition: The date the run was processed by USGS researchers.
Attribute_Definition_Source: USGS
Attribute_Domain_Values:
Range_Domain:
Range_Domain_Minimum: 05/5/2019
Range_Domain_Maximum: 05/15/2019
Attribute_Units_of_Measure: Dates in MM/DD/YYYY format
Attribute:
Attribute_Label: Test Name
Attribute_Definition:
Unique alpha-numeric identifier assigned to each sample by Qubit 3.0
Attribute_Definition_Source: USGS
Attribute_Domain_Values:
Range_Domain:
Range_Domain_Minimum: Sample_#190505-174736
Range_Domain_Maximum: Sample_#190515-170555
Attribute_Units_of_Measure: N/A
Attribute:
Attribute_Label: Sample Number
Attribute_Definition:
This is a U.S. Geological Survey, Coastal and Marine Science Center alphanumeric label that uniquely identifies each sample. Three numbers identify the sample.
Attribute_Definition_Source: USGS
Attribute_Domain_Values:
Range_Domain:
Range_Domain_Minimum: 207
Range_Domain_Maximum: 497
Attribute_Units_of_Measure: N/A
Attribute:
Attribute_Label: Sample Location
Attribute_Definition: The is the study site at which the sample was collected.
Attribute_Definition_Source: USGS
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: CRK
Enumerated_Domain_Value_Definition: Crocker Reef
Enumerated_Domain_Value_Definition_Source: USGS
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: FWY
Enumerated_Domain_Value_Definition: Fowey Rocks
Enumerated_Domain_Value_Definition_Source: USGS
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: SMK
Enumerated_Domain_Value_Definition: Sombrero Reef
Enumerated_Domain_Value_Definition_Source: USGS
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: PLS
Enumerated_Domain_Value_Definition: Pulaski Shoal
Enumerated_Domain_Value_Definition_Source: USGS
Attribute:
Attribute_Label: Qubit tube concentration (ng/mL)
Attribute_Definition:
The concentration of double-stranded DNA in the assay tube in nanograms per milliliter (ng/mL).
Attribute_Definition_Source: USGS
Attribute_Domain_Values:
Range_Domain:
Range_Domain_Minimum: 0.93
Range_Domain_Maximum: 495
Attribute_Units_of_Measure: ng/mL
Attribute:
Attribute_Label: Original sample concentration (ng/mL)
Attribute_Definition:
The concentration of the original sample DNA as calculated by Qubit 3.0 in nanograms per milliliter (ng/mL).
Attribute_Definition_Source: USGS
Attribute_Domain_Values:
Range_Domain:
Range_Domain_Minimum: 186
Range_Domain_Maximum: 99000
Attribute_Units_of_Measure: ng/mL
Attribute:
Attribute_Label: Sample volume (μL)
Attribute_Definition:
The volume of original sample used in the assay in microliters (μL).
Attribute_Definition_Source: USGS
Attribute_Domain_Values:
Range_Domain:
Range_Domain_Minimum: 1
Range_Domain_Maximum: 1
Attribute_Units_of_Measure: μL
Distribution_Information:
Distributor:
Contact_Information:
Contact_Person_Primary:
Contact_Person: Lauren T. Toth
Contact_Organization:
U.S. Geological Survey, St. Petersburg Coastal and Marine Science Center
Contact_Position: Research Physical Scientist
Contact_Address:
Address_Type: mailing and physical
Address: 600 4Th Street South
City: St. Petersburg
State_or_Province: FL
Postal_Code: 33701
Country: US
Contact_Voice_Telephone: 727-502-8029
Contact_Electronic_Mail_Address: ltoth@usgs.gov
Distribution_Liability:
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.
Standard_Order_Process:
Digital_Form:
Digital_Transfer_Information:
Format_Name: CSV, XLSX
Digital_Transfer_Option:
Fees: None
Metadata_Reference_Information:
Metadata_Date: 20210713
Metadata_Contact:
Contact_Information:
Contact_Person_Primary:
Contact_Person: Lauren T. Toth
Contact_Organization:
U.S. Geological Survey, St. Petersburg Coastal and Marine Science Center
Contact_Position: Research Physical Scientist
Contact_Address:
Address_Type: mailing and physical
Address: 600 4Th Street South
City: St. Petersburg
State_or_Province: Florida
Postal_Code: 33701
Country: United States
Contact_Voice_Telephone: 727-502-8029
Contact_Electronic_Mail_Address: ltoth@usgs.gov
Metadata_Standard_Name: Content Standard for Digital Geospatial Metadata
Metadata_Standard_Version: FGDC-STD-001-1998

This page is <https://cmgds.marine.usgs.gov/catalog/spcmsc/Porites_astreoides_metadata.html>
Generated by mp version 2.9.50 on Tue Sep 21 18:18:51 2021