Metadata: Identification_Information: Citation: Citation_Information: Originator: Christina A. Kellogg Originator: Julie J. Voelschow Publication_Date: 20260217 Title: Screening Coral Tissue Samples (Colpophyllia natans) Collected From the Florida Keys Using a Quantitative Polymerase Chain Reaction (qPCR) Antibiotic Resistance Gene Microarray – Raw Data Geospatial_Data_Presentation_Form: tabular digital data Larger_Work_Citation: Citation_Information: Originator: Christina A. Kellogg Originator: Julie J. Voelschow Publication_Date: 20260217 Title: Screening Coral Tissue Samples (Colpophyllia natans) Collected From the Florida Keys Using a Quantitative Polymerase Chain Reaction (qPCR) Antibiotic Resistance Gene Microarray – Raw Data Geospatial_Data_Presentation_Form: tabular digital data Series_Information: Series_Name: U.S. Geological Survey data release Issue_Identification: doi:10.5066/P9AST28V 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/P9AST28V Description: Abstract: The files in this data release are those referenced in the journal article by Neely and others (2026) entitled "Assessment of antibiotic resistance genes in Caribbean corals, including those treated with amoxicillin." They represent the raw fluorescence data and threshold cycle (Ct) data generated from quantitative polymerase chain reaction (qPCR) microarray runs using deoxyribonucleic acid (DNA) extractions from 12 coral (Colpophyllia natans) samples as templates. These files were produced by the Applied Biosystems StepOnePlus™ Real-Time PCR System Software (version 2.2.2). The coral tissue samples were collected on November 17th, 2022, from Cheeca Rocks in the Florida Keys from depths ranging from 9 to 13 feet (2.7 to 4.0 meters). The samples were collected purpose of determining whether there is a higher incidence or diversity of microbial antibiotic resistance genes (ARG) in corals that have previously been treated for stony coral tissue loss disease (SCTLD) with amoxicillin base2B as compared to untreated coral. Tissue samples were preserved in RNAlater, and frozen until shipped for processing. The frozen coral samples were sent from Nova Southeastern University (Fort Lauderdale, Florida) and received on November 23rd 2022, by the U.S. Geological Survey St. Petersburg Coastal and Marine Science Center (USGS SPCMSC) Coral Microbial Ecology Laboratory in St. Petersburg, Florida (FL), USA, and immediately frozen at minus twenty degrees Celsius (-20°C) until processing. Microbial DNA extractions from the coral samples were performed on December 13th 2022, using a Qiagen Dneasy PowerBiofilm kit. All qPCR runs were performed between January and February 2023 on an Applied Biosystems StepOnePlus™ Real-Time PCR System, using Qiagen Microbial DNA qPCR Arrays ARG (BAID-1901ZRC-24), and data files were exported as Microsoft Excel files (.xls) and converted into comma-separated values (.csv) files. The data files were then edited to remove columns that contained no values, or that did not apply to this dataset. Purpose: The purpose of this experiment was to examine whether there is a higher incidence or diversity of microbial antibiotic resistance genes in corals that have been previously treated for SCTLD with amoxicillin base 2B as compared to untreated corals. Supplemental_Information: Coral samples were collected under Field Activity Number (FAN) 2022-343-DD. FANs are unique identifiers assigned by the U.S. Geological Survey (USGS) to provide more information about the activities conducted in the field for a study. Please visit the Coastal and Marine Geoscience Data System (CMGDS) field activity webpage for more information about each FAN related to this dataset, https://cmgds.marine.usgs.gov/services/activity.php?fan=2022-343-DD. Block Type: 96well Chemistry: TAQMAN Experiment Run timeframe: January and February 2023 Instrument Type: steponeplus Passive Reference: ROX Analysis Type: Singleplex Endogenous Control: Pan Bacteria 1.1, Pan Bacteria 1.2, Pan Bacteria 1.3, Pan Bacteria 3.1, Pan Bacteria 3.2, Pan Bacteria 3.3 RQ Min/Max Confidence Level 95.0 Time_Period_of_Content: Time_Period_Information: Range_of_Dates/Times: Beginning_Date: 20221117 Ending_Date: 20230217 Currentness_Reference: ground condition Status: Progress: Complete Maintenance_and_Update_Frequency: None planned Spatial_Domain: Description_of_Geographic_Extent: Florida Keys Bounding_Coordinates: West_Bounding_Coordinate: -80.625280 East_Bounding_Coordinate: -80.616667 North_Bounding_Coordinate: 24.911667 South_Bounding_Coordinate: 24.902778 Keywords: Theme: Theme_Keyword_Thesaurus: USGS Metadata Identifier Theme_Keyword: USGS:e0e10791-cd17-4bc1-921b-e1ebbe276674 Theme: Theme_Keyword_Thesaurus: ISO 19115 Topic Category Theme_Keyword: biota Theme_Keyword: oceans Theme: Theme_Keyword_Thesaurus: USGS Thesaurus Theme_Keyword: bacteria Theme_Keyword: polymerase chain reaction Theme_Keyword: microbiology Theme_Keyword: coelenterates Theme: Theme_Keyword_Thesaurus: None Theme_Keyword: antibiotic resistance genes Theme_Keyword: quantitative polymerase chain reaction Place: Place_Keyword_Thesaurus: Geographic Names Information System (GNIS) Place_Keyword: Florida Keys Place_Keyword: State of Florida Access_Constraints: No access constraints. Please see 'Distribution Information' for details. Use_Constraints: These data are marked with a Creative Commons CC0 1.0 Universal License. These data are in the public domain and do not have any use constraints. Users are advised to read the dataset's metadata thoroughly to understand appropriate use and data limitations. Point_of_Contact: Contact_Information: Contact_Person_Primary: Contact_Person: Christina A. Kellogg Contact_Organization: U.S. Geological Survey Contact_Position: Research Microbiologist Contact_Address: Address_Type: mailing Address: 600 4th St. South City: St. Petersburg State_or_Province: Florida Postal_Code: 33701 Country: United States Contact_Voice_Telephone: 727-502-8128 Contact_Electronic_Mail_Address: ckellogg@usgs.gov Native_Data_Set_Environment: Environment as of Metadata Creation: MacOS Ventura 13.6.6, Applied Biosystems StepOnePlus™ Real-Time PCR System Software (version 2.2.2). Cross_Reference: Citation_Information: Originator: Qiagen Publication_Date: 20200131 Title: Qiagen DNeasy PowerBiofilm kit handbook Geospatial_Data_Presentation_Form: Instructional Manual Online_Linkage: https://www.qiagen.com/us/resources/download.aspx?id=c5363245-cd9c-4314-b8fb-c4f8b4d669c4&lang=en Cross_Reference: Citation_Information: Originator: Qiagen GeneGlobe Publication_Date: 20220731 Title: Microbial DNA qPCR Instructions for Use: For real-time PCR-based profiling/detection of microbial species, antibiotic resistance genes or virulence factor genes Geospatial_Data_Presentation_Form: Instructional Manual Online_Linkage: https://www.qiagen.com/us/resources/resourcedetail?id=e4e55f41-52c3-424e-83d2-0d20fa577435&lang=en Cross_Reference: Citation_Information: Originator: Karen L. Neely Originator: Christina A. Kellogg Originator: Julie J. Voelschow Originator: Allison R. Cauvin Originator: Sydney A. M. Reed Originator: Ewelina Rubin Originator: Julie L. Meyer Publication_Date: 20260216 Title: Assessment of antibiotic resistance genes in Caribbean corals, including those treated with amoxicillin Geospatial_Data_Presentation_Form: publication Series_Information: Series_Name: Coral Reefs Issue_Identification: Unknown Online_Linkage: https://doi.org/10.1007/s00338-026-02832-z Data_Quality_Information: Attribute_Accuracy: Attribute_Accuracy_Report: Each array contains endogenous controls (Pan Bacteria 1.1, Pan Bacteria 1.2, Pan Bacteria 1.3, Pan Bacteria 3.1, Pan Bacteria 3.2, and Pan Bacteria 3.3) meant to standardize data processing for each run. Logical_Consistency_Report: Each array contains positive controls (PPC 1, PPC 2, and PPC 3) to detect inhibition. Completeness_Report: Dataset is considered complete for the information presented, as described in the abstract. Lineage: Process_Step: Process_Description: Coral collection and preservation: The coral samples were collected on November 17th, 2022 from Cheeca Rocks in the Florida Keys from depths ranging from 9 to 13 feet (2.7 to 4.0 meters). Four of the samples collected had never been treated with the antibiotic (amoxicillin base2B) used to treat for SCTLD, four had been treated once, and four had been treated several times. Coral samples were preserved in RNAlater, and frozen until processed. A sample inventory data file (Cnat2022_ARG_SampleInventory) is also included in this release to provide collection details about the coral samples used in this study. Process_Date: 20221117 Source_Produced_Citation_Abbreviation: Cnat2022_ARG_SampleInventory.csv Source_Produced_Citation_Abbreviation: Cnat2022_ARG_SampleInventory.xlsx Process_Step: Process_Description: DNA extraction: The frozen coral samples were sent from Nova Southeastern University in Fort Lauderdale, FL and received on November 23rd, 2022, by the USGS SPCMSC Coral Microbial Ecology Laboratory in St. Petersburg, FL and immediately frozen at -20°C until processing. Microbial DNA extractions from the coral samples were performed on December 13th 2022, using a Qiagen DNeasy PowerBiofilm kit (Qiagen, 2020). Process_Date: 20221215 Process_Step: Process_Description: qPCR runs: DNA quantification was performed for the extractions (Qubit 3 Fluorometer, Invitrogen) to determine what volume of the template DNA would be used for each reaction master mix. Between 1100 to 10246 nanograms (ng) from each extraction was used to create the master mix for each plate. All qPCR runs were performed on an Applied Biosystems StepOnePlus™ Real-Time PCR System, using Qiagen Microbial DNA qPCR Arrays ARG (Qiagen, 2022). Each run produced raw fluorescence data and threshold cycle data files, that were exported as Microsoft Excel files (.xls) and were then converted to comma-separated values (.csv) files, for inclusion in this data release. The raw fluorescence (Cnat#_RawFluor) and threshold cycle data (Cnat#_Ct) files were organized into individual .csv files with 12 data files per data type. Please see the accompanying data dictionary (.docx) for more information about these data files. These files are referenced in the journal article (Neely and others, 2026). Process_Date: 20230217 Source_Produced_Citation_Abbreviation: Cnat2022_ARG_Ct.zip Source_Produced_Citation_Abbreviation: Cnat2022_ARG_RawFluorescence.zip Entity_and_Attribute_Information: Detailed_Description: Entity_Type: Entity_Type_Label: Cnat2022_ARG_SampleInventory Entity_Type_Definition: Comma-separated values (.csv) and Microsoft Excel Worksheet (.xlsx) files containing collection and sample information about the coral samples collected from Cheeca Rocks on November 17th 2022 used in the qPCR analysis. Entity_Type_Definition_Source: USGS Attribute: Attribute_Label: Date Attribute_Definition: The date the coral sample was collected. Attribute_Definition_Source: USGS Attribute_Domain_Values: Enumerated_Domain: Enumerated_Domain_Value: 11/17/2022 Enumerated_Domain_Value_Definition: The date the coral sample was collected in the format of MM/DD/YYYY Enumerated_Domain_Value_Definition_Source: USGS Attribute: Attribute_Label: Site Attribute_Definition: The location the coral sample was collected. Attribute_Definition_Source: USGS Attribute_Domain_Values: Enumerated_Domain: Enumerated_Domain_Value: Cheeca Rocks, Florida Keys Enumerated_Domain_Value_Definition: The coral samples were collected at Cheeca Rocks, Florida Keys. Enumerated_Domain_Value_Definition_Source: USGS Attribute: Attribute_Label: Bag # Attribute_Definition: A unique identifier used to organize the sample. Attribute_Definition_Source: USGS Attribute_Domain_Values: Range_Domain: Range_Domain_Minimum: 2 Range_Domain_Maximum: 24 Attribute: Attribute_Label: Species Attribute_Definition: Species of coral. Attribute_Definition_Source: USGS Attribute_Domain_Values: Enumerated_Domain: Enumerated_Domain_Value: CNAT Enumerated_Domain_Value_Definition: CNAT was used as an abbreviation for the coral species Colpophyllia natans. Enumerated_Domain_Value_Definition_Source: USGS Attribute: Attribute_Label: Status Attribute_Definition: Determination of whether the coral had previously been treated with the antibiotic amoxicillin base2B. The samples were untreated, treated once, or treated several times. Attribute_Definition_Source: USGS Attribute_Domain_Values: Enumerated_Domain: Enumerated_Domain_Value: Never treated Enumerated_Domain_Value_Definition: The sample was never treated with amoxicillin base2B. Enumerated_Domain_Value_Definition_Source: USGS Attribute_Domain_Values: Enumerated_Domain: Enumerated_Domain_Value: Treated once Enumerated_Domain_Value_Definition: The sample had been treated once with amoxicillin base2B. Enumerated_Domain_Value_Definition_Source: USGS Attribute_Domain_Values: Enumerated_Domain: Enumerated_Domain_Value: Treated many Enumerated_Domain_Value_Definition: The sample had been treated more than once with amoxicillin base2B. Enumerated_Domain_Value_Definition_Source: USGS Attribute: Attribute_Label: Depth (ft) Attribute_Definition: The depth at which the coral samples were collected in feet. Attribute_Definition_Source: USGS Attribute_Domain_Values: Range_Domain: Range_Domain_Minimum: 9 Range_Domain_Maximum: 13 Attribute_Units_of_Measure: feet Attribute: Attribute_Label: DNA concentration applied to array (ng) Attribute_Definition: The amount of extracted DNA used to create the master mix for the sample's qPCR run, in nanograms. Attribute_Definition_Source: USGS Attribute_Domain_Values: Range_Domain: Range_Domain_Minimum: 1100 Range_Domain_Maximum: 10246 Attribute_Units_of_Measure: nanograms Overview_Description: Entity_and_Attribute_Overview: The detailed attribute descriptions for the 12 raw fluorescence (Cnat2022_ARG_RawFluorescence.zip) and threshold cycle data files (Cnat2022_ARG_Ct.zip) are provided in the included data dictionary (Cnat2022_ARG_DataDictionary.docx). These metadata are not complete without this file, and users should refer to the data dictionary when viewing the data file. Entity_and_Attribute_Detail_Citation: The entity and attribute information were generated by the individual and/or agency identified as the originator of the dataset. Please review the rest of the metadata record for additional details and information. Distribution_Information: Distributor: Contact_Information: Contact_Person_Primary: Contact_Person: USGS SPCMSC Data Management Contact_Organization: U.S. Geological Survey, St. Petersburg Coastal and Marine Science Center Contact_Address: Address_Type: mailing Address: 600 4th St. South City: St. Petersburg State_or_Province: Florida Postal_Code: 33701 Country: United States Contact_Voice_Telephone: 727-502-8000 Contact_Electronic_Mail_Address: gs-g-spcmsc_data_inquiries@usgs.gov Resource_Description: Cnat#_RawFluor.csv, Cnat#_Ct.csv, Cnat2022_ARG_SampleInventory.csv, Cnat2022_ARG_SampleInventory.xlsx, Cnat2022_ARG_DataDictionary.docx 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 for other purposes, nor on all computer systems, 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. Standard_Order_Process: Digital_Form: Digital_Transfer_Information: Format_Name: comma-delimited text, Microsoft Excel format, Microsoft Word format Digital_Transfer_Option: Online_Option: Computer_Contact_Information: Network_Address: Network_Resource_Name: https://coastal.er.usgs.gov/data-release/doi-P9AST28V/data/Cnat2022_ARG_Ct.zip Network_Resource_Name: https://coastal.er.usgs.gov/data-release/doi-P9AST28V/data/Cnat2022_ARG_RawFluorescence.zip Fees: None Metadata_Reference_Information: Metadata_Date: 20260217 Metadata_Contact: Contact_Information: Contact_Person_Primary: Contact_Person: USGS SPCMSC Data Management Contact_Organization: U.S. Geological Survey, St. Petersburg Coastal and Marine Science Center Contact_Address: Address_Type: mailing Address: 600 4th St. South City: St. Petersburg State_or_Province: Florida Postal_Code: 33701 Country: United States Contact_Voice_Telephone: 727-502-8000 Contact_Electronic_Mail_Address: gs-g-spcmsc_data_inquiries@usgs.gov Metadata_Standard_Name: FGDC Biological Data Profile of the Content Standard for Digital Geospatial Metadata Metadata_Standard_Version: FGDC-STD-001.1-1999