The files in this data release 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" (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 metabolic categories: carbon, sulfur, and nitrogen cycling as well as metal homeostasis, antibiotic resistance, and contaminant degradation. One microarray was run for each coral sample (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. Corals were collected during research cruises in August 2018 and April 2019, from sites offshore of the southeastern coast of the United States in water depths ranging from 296-1567 meters. Coral samples were flash frozen in liquid nitrogen on the ship and stored at -80 degrees Celsius until processed. Extraction of 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. DNA samples were sent to Glomics, Inc. on August 6, 2019, for application to GeoChip 5.0S microarrays. For more information, please see the metadata files.


Pratte, Z.A., Stewart, F. J., and Kellogg, C.A., 2023, Functional gene composition and metabolic potential of deep-sea coral-associated microbial communities: Coral Reefs, https://doi.org/10.1007/s00338-023-02409-0.

For more information, you may contact Christina Kellogg at the USGS St. Petersburg Coastal and Marine Science Center, 600 4th Street South, St. Petersburg, Florida, USA, 33710; Telephone: (727) 502-8128; Email: ckellogg@usgs.gov.

The file labeled "GeoChip_raw_data.zip" contains two files, Kellogg_GeoChip_Data (.csv, .txt, .xlsx) and Kellogg_GeoChip_SampleInfo (.csv, .txt, .xlsx). Kellogg_GeoChip_Data contains a tabulation of microarray normalized signal intensity values for each sample and the control blank, listed by each probe spot's unique identification number, gene category, sub-categories, and associated phylogenetic information. Only those probes (out of the 57,498 total available on each GeoChip) that were above Glomic's cutoff values of signal-to-noise ratio greater than or equal to 2, and occurring in at least one sample are listed. Kellogg_GeoChip_SampleInfo contains a list of field sample collection information connected to the DNA samples which were applied to the GeoChip microarrays, including coral species, collection site, depth, latitude, longitude, temperature, salinity, and links the GeoChip ID to the cruise sample and journal article designations for the same samples.



The column headers in the data file Kellogg_GeoChip_Data are defined below. An entry of "N/A" is defined as "not applicable".

uniqueID: Numerical designation for each probe on the GeoChip 5.0S microarray.

proteinGI: Numerical designation for each probe on the GeoChip 5.0S microarray.

accessionNo: GenBank (National Center for Biotechnology Information at www.ncbi.nlm.nih.gov) accession number for the sequence from which the probe is derived.

gene: Name of the gene the probe targets.

species: Species of microbe (if known) in which the gene the probe targets is found.

lineage: Taxonomic information about the microbe in which the gene the probe targets is found; includes superkingdom, phylum, class, order, family, genus, species.

annotation: Any functional or structural information about the gene.

geneCategory: Top level grouping of gene functions included on the GeoChip 5.0S microarray; includes Carbon Cycling, Metal Homeostatis, Organic Remediation, Phylogeny, Nitrogen Cycling, Phosphorus Cycling, Sulfur Cycling, and Virulence.

subcategory1: Specific function of gene category.

subcategory2: Additional information about functional genes, such as substrate the encoded enzyme acts upon or metabolic pathway that includes functional gene.

MA_01: GeoChip sample identifier within the raw data file; Desmophyllum pertusum L1.

MA_02: GeoChip sample identifier within the raw data file; Desmophyllum pertusum L2.

MA_03: GeoChip sample identifier within the raw data file; Desmophyllum pertusum L3.

MA_04: GeoChip sample identifier within the raw data file; Enallopsammia profounda E1.

MA_05: GeoChip sample identifier within the raw data file; Enallopsammia profounda E2.

MA_06: GeoChip sample identifier within the raw data file; Enallopsammia profunda E3.

MA_07: GeoChip sample identifier within the raw data file; Desmophyllum dianthus D1.

MA_08: GeoChip sample identifier within the raw data file; Desmophyllum dianthus D2.

MA_09: GeoChip sample identifier within the raw data file; Desmophyllum dianthus D3.

MA_10: GeoChip sample identifier within the raw data file; Acanthogorgia spissa A1.

MA_11: GeoChip sample identifier within the raw data file; Acanthogorgia aspera A2.

MA_12: GeoChip sample identifier within the raw data file; control blank.

The column headers in the data file GeoChip_SampleInfo are defined below. An entry of "N/A" is defined as "not applicable".

Sample Type: Deep-sea coral genus and species name or control blank from which DNA was extracted for application to the GeoChip 5.0S microarrays.

Site: Geographic location where the coral sample was collected.

Cruise Sample ID: Individual sample identifier with respect to the research cruise on which the sample was collected.

Depth (m): Depth of water in meters at which the sample was collected.

Latitude (°N): The latitudinal geographical coordinates of the location where the sample was collected, in digital degrees North.

Longitude (°W): The longitudinal geographical coordinates of the location where the sample was collected, in digital degrees West.

Temp (°C): Temperature, in degrees Celsius, at which the sample was collected.

Salinity (ppt): The amount of dissolved salts in the water during which the sample was collected. Measured in parts per thousand.

Collection Date (yyyymmdd): The date on which the sample was collected, formatted as year, month, day. 

GeoChip ID (journal): Individual sample identifier as listed in the journal article (Pratte and others, 2023).

GeoChip ID (raw data): Individual sample identifier as listed within the raw data file.