In accordance with SO #3423 - The Gulf of America and SO #3424 - Mount McKinley and Landmarks Honoring the Alaskan People, new USGS data releases specific to those named places will utilize the new name Gulf of America and the restored name Mount McKinley. Per USGS practice, historical data will retain the name of the geographic features as they were known at the time the data were originally released.
Data Release
Cold-water Coral Microbiomes (Acanthogorgia spp., Desmophyllum dianthus, and Lophelia pertusa) from the Gulf of Mexico and Atlantic Ocean off the Southeast Coast of the United States—Raw Data
By Christina A. Kellogg and Julie J. Voelschow
USGS, St. Petersburg, Florida
Summary
The files in this data release are the raw 16S rRNA gene amplicon DNA sequence files from 28 samples of deep-sea corals Acanthogorgia aspera, Acanthogorgia spissa, Desmophyllum dianthus, and Lophelia pertusa, as well as an extraction blank for the Qiagen PowerBiofilm kit used for DNA extraction. The samples were collected during four research cruises from various locations in the Gulf of Mexico and the Atlantic Ocean off the east coast of the United States in deep-sea coral ecosystems from 2013 to 2019 for microbial analysis.
Extraction of DNA from the samples occurred at the USGS Coral Microbial Ecology Laboratory in St. Petersburg, FL, using Qiagen’s DNeasy PowerBiofilm kit. PCR amplification and sequencing were performed by RTSF Genomics Core at Michigan State University using primers 341F/806R to target the V3-V4 region of the 16S rRNA gene on a MiSeq sequencing system with v2 chemistry to obtain paired-end 250-bp reads. The raw data files associated with this data release have also been submitted to the NCBI Sequence Read Archive under BioProject number PRJNA699458. For more information, please see the README file and metadata files.
Kellogg, C.A. and Pratte, Z.A., 2021, Unexpected diversity of Endozoicomonas in deep-sea corals: Marine Ecology Progress Series, v.673, article 13844, 15 p., https://doi.org/10.3354/meps13844.
Data
| File Name and Description | Metadata (XML format) | Metadata (text format) | Download File |
|---|---|---|---|
| PRJNA699458_16S-V3V4_raw_data_1.zip Zip file containing raw sequencing data (FASTQ) and MIMARKS-compliant sampling metadata (.csv, .txt, .xlsx) |
PRJNA699458_FGDC_metadata.xml | PRJNA699458_FGDC_metadata.txt | PRJNA699458_16S-V3V4_raw_data_1.zip (3.05 GB) |
| Supplemental information | |||
| README_PRJNA699458.txt Readme file explaining data (.txt) |
Not applicable | Not applicable | README_PRJNA699458.txt (4 KB) |
| PRJNA699458_MIMARKS.zip MIMARKS-compliant sampling metadata (.csv, .txt, .xlsx) |
Not applicable | Not applicable | PRJNA699458_MIMARKS.zip (21 KB) |
| PRJNA699458_SRA_metadata.zip Laboratory process metadata (.xlsx, .csv) |
Not applicable | Not applicable | PRJNA699458_SRA_metadata.zip (49 KB) |
Figure 1. Locations of study areas in the Atlantic Ocean and Gulf of Mexico.
Suggested Citation
Kellogg, C.A. and Voelschow, J.J., 2021, Cold-water coral microbiomes (Acanthogorgia spp., Desmophyllum dianthus, and Lophelia pertusa) from the Gulf of Mexico and Atlantic Ocean off the southeast coast of the United States—raw data: U.S. Geological Survey data release, https://doi.org/10.5066/P9Z1HPKR.