Functional gene microarray data from cold-water corals (Acanthogorgia spp., Desmophyllum dianthus, Desmophyllum pertusum, and Enallopsammia profunda) from the Atlantic Ocean off the Southeast Coast of the United States–Raw Data and Sample Site Information

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Frequently anticipated questions:

What does this data set describe?

Title:
Functional gene microarray data from cold-water corals (Acanthogorgia spp., Desmophyllum dianthus, Desmophyllum pertusum, and Enallopsammia profunda) from the Atlantic Ocean off the Southeast Coast of the United States–Raw Data and Sample Site Information
Abstract:
The files in this data release (Kellogg and Voelschow, 2023) contain normalized microarray probe intensity values from GeoChip 5.0S microarrays referenced in the journal article entitled “Functional gene composition and metabolic potential of deep-sea coral-associated microbial communities” by Pratte and others (2023). The GeoChip 5.0S microarrays, provided by Glomics Inc., contain 57,498 oligonucleotide probes that target 383 microbial (archaeal, bacterial, and fungal) genes and cover 151,797 coding sequences within the following metabolic categories: carbon, sulfur, and nitrogen cycling, as well as metal homeostasis, antibiotic resistance, and contaminant degradation. One microarray was run per coral (number of samples [n] = 11), using 400 nanograms (ng) of DNA extracted from the sample, plus a microarray run as a reagent blank (n = 1). The coral samples included one Acanthogorgia aspera, one Acanthogorgia spissa, three Desmophyllum dianthus, three Desmophyllum pertusum (formerly Lophelia pertusa) and three Enallopsammia profounda species. Corals were collected during two research cruises: the first in August 2018 and the second in April 2019, from six sites offshore of the southeastern coast of the United States in water depths ranging from 296–1567 meters (m). Coral samples were flash frozen in liquid nitrogen on the ship and stored at -80 degrees Celsius (°C) until processed. Extraction of deoxyribose nucleic acid (DNA) from the coral samples and kit blank occurred on August 5, 2019, at the Coral Microbial Ecology Laboratory in St. Petersburg, Florida (FL) using a QIAGEN DNeasy PowerBiofilm kit. Then, DNA samples were sent to Glomics Inc. on August 6, 2019, for application of GeoChip 5.0S microarrays. For more information, please see the README file and metadata files.
Supplemental_Information:
Coral samples were collected under Field Activity Number (FAN) 2018-042-FA and 2019-314-FA. 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/fan_info.php?fan=2018-042-FA and https://cmgds.marine.usgs.gov/fan_info.php?fan=2019-314-FA.
  1. How might this data set be cited?
    Kellogg, Christina A., and Voelschow, Julie J., 20230814, Functional gene microarray data from cold-water corals (Acanthogorgia spp., Desmophyllum dianthus, Desmophyllum pertusum, and Enallopsammia profunda) from the Atlantic Ocean off the Southeast Coast of the United States–Raw Data and Sample Site Information:.

    This is part of the following larger work.

    Kellogg, Christina A., and Voelschow, Julie J., 20230814, Functional Gene Microarray Data From Cold-water Corals (Acanthogorgia spp., Desmophyllum dianthus, Desmophyllum pertusum, and Enallopsammia profunda) From the Atlantic Ocean off the Southeast Coast of the United States–Raw Data: US Geological Survey data release doi:10.5066/P9RPE8YX, 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: -79.19408
    East_Bounding_Coordinate: -75.15013
    North_Bounding_Coordinate: 34.93145
    South_Bounding_Coordinate: 31.2876
    Description_of_Geographic_Extent: Atlantic Ocean
  3. What does it look like?
  4. Does the data set describe conditions during a particular time period?
    Beginning_Date: 24-Aug-2018
    Ending_Date: 29-Apr-2019
    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?
      This is a Point data set. It contains the following vector data types (SDTS terminology):
      • Point (11)
    2. What coordinate system is used to represent geographic features?
      Horizontal positions are specified in geographic coordinates, that is, latitude and longitude. Latitudes are given to the nearest 0.0197864699. Longitudes are given to the nearest 0.0228595953. Latitude and longitude values are specified in Decimal degrees. The horizontal datum used is World Geodetic System of 1984.
      The ellipsoid used is WGS_1984.
      The semi-major axis of the ellipsoid used is 6378137.0.
      The flattening of the ellipsoid used is 1/298.257223563.
      Vertical_Coordinate_System_Definition:
      Altitude_System_Definition:
      Altitude_Datum_Name: North American Vertical Datum 1988
      Altitude_Resolution: 0.01
      Altitude_Distance_Units: meters
      Altitude_Encoding_Method: Attribute values
  7. How does the data set describe geographic features?
    Entity_and_Attribute_Overview:
    Please refer to the "README" file, README_GeoChip.txt, for detailed descriptions of the contents of the GeoChip raw and processed data files. Additional information is contained in the metadata files.
    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 - St. Petersburg Coastal and Marine Science Center
    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 identify microbial functional genes associated with deep-sea, cold-water corals in the Atlantic.

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: 25-Apr-2019 (process 1 of 4)
    Sample collection: Coral samples were collected during two research cruises, one in 2018 and the other in 2019, from sites off the southeastern coast of the United States (Cape Lookout, Pamlico Canyon, Blake Escarpment, Richardson Ridge, Pea Island Seep, and Savannah Bank) supporting the DeepSEARCH project. Samples from 2018 were collected using the submersible 'Alvin' and support vessel research vessel (RV) 'Atlantis', and the samples from 2019 were collected using the remotely-operated vehicle (ROV) 'Jason II' from the National Oceanic and Atmospheric Administration's (NOAA) ship 'Ronald H. Brown'. Person who carried out this activity:
    Christina A. Kellogg
    U.S. Geological Survey - St. Petersburg Coastal and Marine Science Center
    Research Microbiologist
    600 4th Street South
    St. Petersburg, FL
    United States

    727-502-8128 (voice)
    ckellogg@usgs.gov
    Date: 25-Apr-2019 (process 2 of 4)
    Sample preparation: On the ship after collection, the coral samples were gently rinsed with 1x phosphate-buffered saline (PBS) to remove surface microbes. Stony coral samples (Desmophyllum dianthus, Desmophyllum pertusum, and Enallopsammia profunda) were placed in a sterile aluminum weigh boats and broken open with a flame sterilized hammer to expose the polyp tissue for processing. Branches of the octocoral samples (Acanthogorgia aspera and Acanthogorgia spissa) were removed for processing using sterile shears. All subsamples were individually wrapped in pre-sterilized aluminum foil, placed into a Whirlpak back and flash frozen in liquid nitrogen, and then transferred to a -80°C freezer when the cruises were over. Person who carried out this activity:
    Christina A. Kellogg
    U.S. Geological Survey - St. Petersburg Coastal and Marine Science Center
    Research Microbiologist
    600 4th Street South
    St. Petersburg, FL
    United States

    727-502-8128 (voice)
    ckellogg@usgs.gov
    Date: 05-Aug-2019 (process 3 of 4)
    DNA extraction: Extraction of DNA occurred at the Coral Microbiology Laboratory in St. Petersburg, Florida in August 2019, using QIAGEN’s DNeasy PowerBiofilm kit. Samples were extracted in duplicate, and then combined at the end for a total of 200 microliters (µL) of DNA solution per coral. QIAGEN’s protocol was followed (edition March 2018) using a vacuum manifold, with few alterations. To compensate for the weight of the skeleton, stony coral samples used 0.2 grams (g) to 0.65 g per extraction tube. Person who carried out this activity:
    Christina A. Kellogg
    U.S. Geological Survey - St. Petersburg Coastal and Marine Science Center
    Research Microbioloigst
    600 4th Street South
    St. Petersburg, FL
    United States

    727-502-8128 (voice)
    ckellogg@usgs.gov
    Date: 25-Sep-2019 (process 4 of 4)
    Processing data: Approximately 180 µL per sample was shipped on dry ice to Glomics Inc. (Norman, Oklahoma) for application to GeoChip 5.0S microarrays. 400 nanograms (ng) of DNA was used directly for labeling, for each sample. The kit blank had an undetectable concentration of DNA, but was labeled using the same process as the samples. Fluorescence-labeling, hybridization of the microarrays, and scanning were carried out as described by Lu and others (2011). Glomics Inc. conducted a data normalization to the samples, and only probed spots that were above a designated limit (a signal-to-noise ratio of greater than or equal to 2 in at least one sample) were retained (Wu, and others 2006; He, and others 2007) Person who carried out this activity:
    Glomics Inc.
    3750 West Main Street, STE AA
    Norman, OK
    United States

    405-312-2900 (voice)
    geochip@glomics.com
  3. What similar or related data should the user be aware of?
    Pratte, Zoe A., Stewart, Frank J., and Kellogg, Christina A., 20230809, Functional gene composition and metabolic potential of deep-sea coral-associated microbial communities: Coral Reefs 2023.

    Online Links:

    QIAGEN, 20200131, QIAGEN DNeasy PowerBiofilm kit handbook.

    Online Links:

    Lu, Zhenmei, Deng, Ye, Joy D. Van Nostrand, He, Zhili, Voordeckers, James, Zhou, Aifen, Lee, Yong-Jin, Mason, Olivia U., Dubinsky, Eric A., Chavarria, Krystle L., Tom, Lauren M., Fortney, Julian L., Lamendella, Regina, Jansson, Janet K., D'haeseleer, Patrik, Hazen, Terry C., and Zhou, Jizhong, 20110804, Microbial gene functions enriched in the Deepwater Horizon deep-sea oil plume: The ISME Journal Volume 6.

    Online Links:

    Other_Citation_Details: Pages 451-460
    He, Zhili, Gentry, Terry J., Schadt, Christopher W., Wu, Liyou, Liebich, Jost, Chong, Song C., Huang, Zhijian, Wu, Weimin, Gu, Baohua, Jardine, Phil, Criddle, Craig, and Zhou, Jizhong, 20070501, GeoChip: a comprehensive microarray for investigating biogeochemical, ecological and environmental processes: The ISME Jounal Volume 1.

    Online Links:

    Other_Citation_Details: Pages 67-77
    Wu, Liyou, Liu, Xueduan, Schadt, Christopher W., and Shou, Jizhong, 20060701, Microarray-based analysis of subnanogram quantities of microbial community DNAs by using whole-community genome amplification: Applied and Environmental Microbiology Volume 72, No. 7.

    Online Links:

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

  1. How well have the observations been checked?
    No formal attribute accuracy tests were conducted.
  2. How accurate are the geographic locations?
    No formal horizontal positional accuracy tests were conducted.
  3. How accurate are the heights or depths?
    No formal vertical positional accuracy tests were conducted.
  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?
    No formal logical accuracy tests were conducted.

How can someone get a copy of the data set?

Are there legal restrictions on access or use of the data?
Access_Constraints None
Use_Constraints None
  1. Who distributes the data set? (Distributor 1 of 1)
    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
  2. What's the catalog number I need to order this data set?
  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 on any other system or for general or scientific purposes, nor shall the act of distribution constitute any such warranty.
  4. How can I download or order the data?

Who wrote the metadata?

Dates:
Last modified: 11-Sep-2023
Metadata author:
Christina A. Kellogg
U.S. Geological Survey - St. Petersburg Coastal and Marine Science Center
Research Microbiologist
600 4th St. South
St. Petersburg, Florida
United States

727-502-8128 (voice)
ckellogg@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/GeoChip_FGDC_metadata.faq.html>
Generated by mp version 2.9.51 on Tue Sep 12 12:19:02 2023