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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Description 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. [More]
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