Screening Coral Tissue Samples (Colpophyllia natans) Collected From the Florida Keys Using a Quantitative Polymerase Chain Reaction (qPCR) Antibiotic Resistance Gene Microarray – Raw Data

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Frequently anticipated questions:

What does this data set describe?

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
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.
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
  1. How might this data set be cited?
    Kellogg, Christina A., and Voelschow, Julie J., 20260217, Screening Coral Tissue Samples (Colpophyllia natans) Collected From the Florida Keys Using a Quantitative Polymerase Chain Reaction (qPCR) Antibiotic Resistance Gene Microarray – Raw Data:.

    This is part of the following larger work.

    Kellogg, Christina A., and Voelschow, Julie J., 20260217, Screening Coral Tissue Samples (Colpophyllia natans) Collected From the Florida Keys Using a Quantitative Polymerase Chain Reaction (qPCR) Antibiotic Resistance Gene Microarray – Raw Data: U.S. Geological Survey data release doi:10.5066/P9AST28V, U.S. Geological Survey - St. Petersburg Coastal and Marine Science Center, St. Petersburg, Florida.

    Online Links:

  2. What geographic area does the data set cover?
    West_Bounding_Coordinate: -80.625280
    East_Bounding_Coordinate: -80.616667
    North_Bounding_Coordinate: 24.911667
    South_Bounding_Coordinate: 24.902778
    Description_of_Geographic_Extent: Florida Keys
  3. What does it look like?
  4. Does the data set describe conditions during a particular time period?
    Beginning_Date: 17-Nov-2022
    Ending_Date: 17-Feb-2023
    Currentness_Reference:
    ground condition
  5. What is the general form of this data set?
    Geospatial_Data_Presentation_Form: tabular digital data
  6. How does the data set represent geographic features?
    1. How are geographic features stored in the data set?
    2. What coordinate system is used to represent geographic features?
  7. How does the data set describe geographic features?
    Cnat2022_ARG_SampleInventory
    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. (Source: USGS)
    Date
    The date the coral sample was collected. (Source: USGS)
    ValueDefinition
    11/17/2022The date the coral sample was collected in the format of MM/DD/YYYY
    Site
    The location the coral sample was collected. (Source: USGS)
    ValueDefinition
    Cheeca Rocks, Florida KeysThe coral samples were collected at Cheeca Rocks, Florida Keys.
    Bag #
    A unique identifier used to organize the sample. (Source: USGS)
    Range of values
    Minimum:2
    Maximum:24
    Species
    Species of coral. (Source: USGS)
    ValueDefinition
    CNATCNAT was used as an abbreviation for the coral species Colpophyllia natans.
    Status
    Determination of whether the coral had previously been treated with the antibiotic amoxicillin base2B. The samples were untreated, treated once, or treated several times. (Source: USGS)
    ValueDefinition
    Never treatedThe sample was never treated with amoxicillin base2B.
    Treated onceThe sample had been treated once with amoxicillin base2B.
    Treated manyThe sample had been treated more than once with amoxicillin base2B.
    Depth (ft)
    The depth at which the coral samples were collected in feet. (Source: USGS)
    Range of values
    Minimum:9
    Maximum:13
    Units:feet
    DNA concentration applied to array (ng)
    The amount of extracted DNA used to create the master mix for the sample's qPCR run, in nanograms. (Source: USGS)
    Range of values
    Minimum:1100
    Maximum:10246
    Units:nanograms
    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.

Who produced the data set?

  1. Who are the originators of the data set? (may include formal authors, digital compilers, and editors)
    • Christina A. Kellogg
    • Julie J. Voelschow
  2. Who also contributed to the data set?
  3. To whom should users address questions about the data?
    Christina A. Kellogg
    U.S. Geological Survey
    Research Microbiologist
    600 4th St. South
    St. Petersburg, Florida
    United States

    727-502-8128 (voice)
    ckellogg@usgs.gov

Why was the data set created?

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.

How was the data set created?

  1. From what previous works were the data drawn?
  2. How were the data generated, processed, and modified?
    Date: 17-Nov-2022 (process 1 of 3)
    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. Data sources produced in this process:
    • Cnat2022_ARG_SampleInventory.csv
    • Cnat2022_ARG_SampleInventory.xlsx
    Date: 15-Dec-2022 (process 2 of 3)
    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).
    Date: 17-Feb-2023 (process 3 of 3)
    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). Data sources produced in this process:
    • Cnat2022_ARG_Ct.zip
    • Cnat2022_ARG_RawFluorescence.zip
  3. What similar or related data should the user be aware of?
    Qiagen, 20200131, Qiagen DNeasy PowerBiofilm kit handbook.

    Online Links:

    GeneGlobe, Qiagen, 20220731, Microbial DNA qPCR Instructions for Use: For real-time PCR-based profiling/detection of microbial species, antibiotic resistance genes or virulence factor genes.

    Online Links:

    Neely, Karen L., Kellogg, Christina A., Voelschow, Julie J., Cauvin, Allison R., M., Sydney A. Reed, Rubin, Ewelina, and Meyer, Julie L., 20260216, Assessment of antibiotic resistance genes in Caribbean corals, including those treated with amoxicillin: Coral Reefs Unknown.

    Online Links:

How reliable are the data; what problems remain in the data set?

  1. How well have the observations been checked?
    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.
  2. How accurate are the geographic locations?
  3. How accurate are the heights or depths?
  4. Where are the gaps in the data? What is missing?
    Dataset is considered complete for the information presented, as described in the abstract.
  5. How consistent are the relationships among the observations, including topology?
    Each array contains positive controls (PPC 1, PPC 2, and PPC 3) to detect inhibition.

How can someone get a copy of the data set?

Are there legal restrictions on access or use of the data?
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.
  1. Who distributes the data set? (Distributor 1 of 1)
    USGS SPCMSC Data Management
    U.S. Geological Survey, St. Petersburg Coastal and Marine Science Center
    600 4th St. South
    St. Petersburg, Florida
    United States

    727-502-8000 (voice)
    gs-g-spcmsc_data_inquiries@usgs.gov
  2. What's the catalog number I need to order this data set? Cnat#_RawFluor.csv, Cnat#_Ct.csv, Cnat2022_ARG_SampleInventory.csv, Cnat2022_ARG_SampleInventory.xlsx, Cnat2022_ARG_DataDictionary.docx
  3. What legal disclaimers am I supposed to read?
    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.
  4. How can I download or order the data?

Who wrote the metadata?

Dates:
Last modified: 17-Feb-2026
Metadata author:
USGS SPCMSC Data Management
U.S. Geological Survey, St. Petersburg Coastal and Marine Science Center
600 4th St. South
St. Petersburg, Florida
United States

727-502-8000 (voice)
gs-g-spcmsc_data_inquiries@usgs.gov
Metadata standard:
FGDC Biological Data Profile of the Content Standard for Digital Geospatial Metadata (FGDC-STD-001.1-1999)
This page is <https://cmgds.marine.usgs.gov/catalog/spcmsc/Cnat2022_ARG_FGDC_metadata.faq.html>
Generated by mp version 2.9.51 on Tue Feb 17 10:37:08 2026