Metadata:
  Identification_Information:
    Citation:
      Citation_Information:
        Originator: Christina A. Kellogg
        Originator: Julie J. Voelschow
        Publication_Date: 20230814
        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
        Geospatial_Data_Presentation_Form: tabular digital data
        Larger_Work_Citation:
          Citation_Information:
            Originator: Christina A. Kellogg
            Originator: Julie J. Voelschow
            Publication_Date: 20230814
            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
            Geospatial_Data_Presentation_Form: tabular digital data
            Series_Information:
              Series_Name: US Geological Survey data release
              Issue_Identification: doi:10.5066/P9RPE8YX
            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/P9RPE8YX
    Description:
      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.
      Purpose: The purpose of this experiment was to identify microbial functional genes associated with deep-sea, cold-water corals in the Atlantic.
      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.
    Time_Period_of_Content:
      Time_Period_Information:
        Range_of_Dates/Times:
          Beginning_Date: 20180824
          Ending_Date: 20190429
      Currentness_Reference: ground condition
    Status:
      Progress: Complete
      Maintenance_and_Update_Frequency: None planned
    Spatial_Domain:
      Description_of_Geographic_Extent: Atlantic Ocean
      Bounding_Coordinates:
        West_Bounding_Coordinate: -79.19408
        East_Bounding_Coordinate: -75.15013
        North_Bounding_Coordinate: 34.93145
        South_Bounding_Coordinate: 31.2876
    Keywords:
      Theme:
        Theme_Keyword_Thesaurus: USGS Metadata Identifier
        Theme_Keyword: USGS:bde2bcd6-a8c3-4397-8d66-99698e57a4c4
      Theme:
        Theme_Keyword_Thesaurus: ISO 19115 Topic Category
        Theme_Keyword: biota
        Theme_Keyword: oceans
      Theme:
        Theme_Keyword_Thesaurus: USGS Thesaurus
        Theme_Keyword: marine biology
        Theme_Keyword: microbiology
        Theme_Keyword: coelenterates
        Theme_Keyword: DNA sequencing
      Place:
        Place_Keyword_Thesaurus: Geographic Names Information System (GNIS)
        Place_Keyword: Atlantic Ocean
      Place:
        Place_Keyword_Thesaurus: None
        Place_Keyword: United States
        Place_Keyword: Pamlico Canyon
        Place_Keyword: Pea Island Seep
        Place_Keyword: Cape Lookout
        Place_Keyword: Richardson Ridge
        Place_Keyword: Blake Deep
        Place_Keyword: Savannah Bank
    Access_Constraints: None
    Use_Constraints: None
    Point_of_Contact:
      Contact_Information:
        Contact_Person_Primary:
          Contact_Person: Christina A. Kellogg
          Contact_Organization: U.S. Geological Survey - St. Petersburg Coastal and Marine Science Center
        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
    Cross_Reference:
      Citation_Information:
        Originator: Zoe A. Pratte
        Originator: Frank J. Stewart
        Originator: Christina A. Kellogg
        Publication_Date: 20230809
        Title: Functional gene composition and metabolic potential of deep-sea coral-associated microbial communities
        Geospatial_Data_Presentation_Form: publication
        Series_Information:
          Series_Name: Coral Reefs
          Issue_Identification: 2023
        Online_Linkage: https://doi.org/10.1007/s00338-023-02409-0
    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: Zhenmei Lu
        Originator: Ye Deng
        Originator: Joy D. Van Nostrand
        Originator: Zhili He
        Originator: James Voordeckers
        Originator: Aifen Zhou
        Originator: Yong-Jin Lee
        Originator: Olivia U. Mason
        Originator: Eric A. Dubinsky
        Originator: Krystle L. Chavarria
        Originator: Lauren M. Tom
        Originator: Julian L. Fortney
        Originator: Regina Lamendella
        Originator: Janet K. Jansson
        Originator: Patrik D'haeseleer
        Originator: Terry C. Hazen
        Originator: Jizhong Zhou
        Publication_Date: 20110804
        Title: Microbial gene functions enriched in the Deepwater Horizon deep-sea oil plume
        Geospatial_Data_Presentation_Form: publication
        Series_Information:
          Series_Name: The ISME Journal
          Issue_Identification: Volume 6
        Other_Citation_Details: Pages 451-460
        Online_Linkage: https://doi.org/10.1038/ismej.2011.91
    Cross_Reference:
      Citation_Information:
        Originator: Zhili He
        Originator: Terry J. Gentry
        Originator: Christopher W. Schadt
        Originator: Liyou Wu
        Originator: Jost Liebich
        Originator: Song C. Chong
        Originator: Zhijian Huang
        Originator: Weimin Wu
        Originator: Baohua Gu
        Originator: Phil Jardine
        Originator: Craig Criddle
        Originator: Jizhong Zhou
        Publication_Date: 20070501
        Title: GeoChip: a comprehensive microarray for investigating biogeochemical, ecological and environmental processes
        Geospatial_Data_Presentation_Form: publication
        Series_Information:
          Series_Name: The ISME Jounal
          Issue_Identification: Volume 1
        Other_Citation_Details: Pages 67-77
        Online_Linkage: https://doi.org/10.1038/ismej.2007.2
    Cross_Reference:
      Citation_Information:
        Originator: Liyou Wu
        Originator: Xueduan Liu
        Originator: Christopher W. Schadt
        Originator: Jizhong Shou
        Publication_Date: 20060701
        Title: Microarray-based analysis of subnanogram quantities of microbial community DNAs by using whole-community genome amplification
        Geospatial_Data_Presentation_Form: publication
        Series_Information:
          Series_Name: Applied and Environmental Microbiology
          Issue_Identification: Volume 72, No. 7
        Online_Linkage: https://doi.org/10.1128/AEM.02738-05
  Data_Quality_Information:
    Attribute_Accuracy:
      Attribute_Accuracy_Report: No formal attribute accuracy tests were conducted.
    Logical_Consistency_Report: No formal logical accuracy tests were conducted.
    Completeness_Report: Dataset is considered complete for the information presented, as described in the abstract.
    Positional_Accuracy:
      Horizontal_Positional_Accuracy:
        Horizontal_Positional_Accuracy_Report: No formal horizontal positional accuracy tests were conducted.
      Vertical_Positional_Accuracy:
        Vertical_Positional_Accuracy_Report: No formal vertical positional accuracy tests were conducted.
    Lineage:
      Process_Step:
        Process_Description: 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'.
        Process_Date: 20190425
        Process_Contact:
          Contact_Information:
            Contact_Person_Primary:
              Contact_Person: Christina A. Kellogg
              Contact_Organization: U.S. Geological Survey - St. Petersburg Coastal and Marine Science Center
            Contact_Position: Research Microbiologist
            Contact_Address:
              Address_Type: mailing and physical
              Address: 600 4th Street South
              City: St. Petersburg
              State_or_Province: FL
              Postal_Code: 33701
              Country: United States
            Contact_Voice_Telephone: 727-502-8128
            Contact_Electronic_Mail_Address: ckellogg@usgs.gov
      Process_Step:
        Process_Description: 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.
        Process_Date: 20190425
        Process_Contact:
          Contact_Information:
            Contact_Person_Primary:
              Contact_Person: Christina A. Kellogg
              Contact_Organization: U.S. Geological Survey - St. Petersburg Coastal and Marine Science Center
            Contact_Position: Research Microbiologist
            Contact_Address:
              Address_Type: mailing and physical
              Address: 600 4th Street South
              City: St. Petersburg
              State_or_Province: FL
              Postal_Code: 33701
              Country: United States
            Contact_Voice_Telephone: 727-502-8128
            Contact_Electronic_Mail_Address: ckellogg@usgs.gov
      Process_Step:
        Process_Description: 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.
        Process_Date: 20190805
        Process_Contact:
          Contact_Information:
            Contact_Person_Primary:
              Contact_Person: Christina A. Kellogg
              Contact_Organization: U.S. Geological Survey - St. Petersburg Coastal and Marine Science Center
            Contact_Position: Research Microbioloigst
            Contact_Address:
              Address_Type: mailing and physical
              Address: 600 4th Street South
              City: St. Petersburg
              State_or_Province: FL
              Postal_Code: 33701
              Country: United States
            Contact_Voice_Telephone: 727-502-8128
            Contact_Electronic_Mail_Address: ckellogg@usgs.gov
      Process_Step:
        Process_Description: 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)
        Process_Date: 20190925
        Process_Contact:
          Contact_Information:
            Contact_Person_Primary:
              Contact_Person: Glomics Inc.
            Contact_Address:
              Address_Type: mailing and physical
              Address: 3750 West Main Street, STE AA
              City: Norman
              State_or_Province: OK
              Postal_Code: 73072
              Country: United States
            Contact_Voice_Telephone: 405-312-2900
            Contact_Electronic_Mail_Address: geochip@glomics.com
  Spatial_Data_Organization_Information:
    Direct_Spatial_Reference_Method: Point
    Point_and_Vector_Object_Information:
      SDTS_Terms_Description:
        SDTS_Point_and_Vector_Object_Type: Point
        Point_and_Vector_Object_Count: 11
  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: World Geodetic System of 1984
        Ellipsoid_Name: WGS_1984
        Semi-major_Axis: 6378137.0
        Denominator_of_Flattening_Ratio: 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
  Entity_and_Attribute_Information:
    Overview_Description:
      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.
  Distribution_Information:
    Distributor:
      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
    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: text, comma-delimited text, Microsoft Excel format
        Digital_Transfer_Option:
          Online_Option:
            Computer_Contact_Information:
              Network_Address:
                Network_Resource_Name: https://coastal.er.usgs.gov/data-release/doi-P9RPE8YX/data/GeoChip_raw_data.zip
      Fees: None
  Metadata_Reference_Information:
    Metadata_Date: 20230911
    Metadata_Contact:
      Contact_Information:
        Contact_Person_Primary:
          Contact_Person: Christina A. Kellogg
          Contact_Organization: U.S. Geological Survey - St. Petersburg Coastal and Marine Science Center
        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
    Metadata_Standard_Name: FGDC Biological Data Profile of the Content Standard for Digital Geospatial Metadata
    Metadata_Standard_Version: FGDC-STD-001.1-1999