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