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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

Metadata Updated: October 28, 2023

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.

Access & Use Information

Public: This dataset is intended for public access and use. License: No license information was provided. If this work was prepared by an officer or employee of the United States government as part of that person's official duties it is considered a U.S. Government Work.

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Dates

Metadata Created Date August 30, 2023
Metadata Updated Date October 28, 2023

Metadata Source

Harvested from DOI EDI

Additional Metadata

Resource Type Dataset
Metadata Created Date August 30, 2023
Metadata Updated Date October 28, 2023
Publisher U.S. Geological Survey
Maintainer
@Id http://datainventory.doi.gov/id/dataset/cee2081686a8c8ad4f6204b519bb3c19
Identifier USGS:bde2bcd6-a8c3-4397-8d66-99698e57a4c4
Data Last Modified 20230911
Category geospatial
Public Access Level public
Bureau Code 010:12
Metadata Context https://project-open-data.cio.gov/v1.1/schema/catalog.jsonld
Metadata Catalog ID https://datainventory.doi.gov/data.json
Schema Version https://project-open-data.cio.gov/v1.1/schema
Catalog Describedby https://project-open-data.cio.gov/v1.1/schema/catalog.json
Harvest Object Id d20a0bd3-400e-4713-bf05-2d3fe8c3d23f
Harvest Source Id 52bfcc16-6e15-478f-809a-b1bc76f1aeda
Harvest Source Title DOI EDI
Metadata Type geospatial
Old Spatial -79.19408,31.2876,-75.15013,34.93145
Publisher Hierarchy White House > U.S. Department of the Interior > U.S. Geological Survey
Source Datajson Identifier True
Source Hash 861d991c1f421bb5b209eb02986f091d0be4ee7b77ca0d1175fd8f4fb53d6655
Source Schema Version 1.1
Spatial {"type": "Polygon", "coordinates": -79.19408, 31.2876, -79.19408, 34.93145, -75.15013, 34.93145, -75.15013, 31.2876, -79.19408, 31.2876}

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