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
Coral Microbiome Preservation and Extraction Method Comparison—Raw Data
By Christina A. Kellogg, Dawn B. Goldsmith, 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 90 samples of tropical and cold-water corals, as well as sequence files from a mock community and extraction blanks for the kits used for DNA extraction. The tropical coral samples (three species) were collected under permit FKNMS-2017-064 (Kellogg) in March 2018 from a nursery in the Florida Keys National Marine Sanctuary and temporarily housed at the facility of Mote Marine Laboratory & Aquarium’s Elizabeth Moore International Center for Coral Reef Research & Restoration in Summerland Key, Florida (FL). The cold-water coral samples (two species) were collected in August 2018 from two locations in the Atlantic Ocean (Pamlico Canyon and Richardson Hills). The purpose of this experiment was to compare preservation and DNA extraction methods across tropical and cold-water corals. Three preservation methods were employed: RNAlater, DNA/RNA Shield, and flash-freezing in liquid nitrogen.
Extraction of DNA from the samples occurred at the Coral Microbial Ecology Laboratory in St. Petersburg, FL using the Qiagen DNeasy PowerBiofilm DNA Isolation Kit and the Promega Maxwell RSC Blood DNA kit . Library preparation and DNA sequencing were conducted by Glomics, Inc. (Norman, Oklahoma) using primers 515F/806RB to target the V4 variable 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 PRJNA544686. For more information, please see the README file and metadata files.
Pratte, Z.A., and Kellogg, C.A, 2021, Comparison of preservation and extraction methods on five taxonomically disparate coral microbiomes: Frontiers in Marine Science, https://doi.org/10.3389/fmars.2021.684161.
Data
| File Name and Description | Metadata (XML format) | Metadata (text format) | Download File |
|---|---|---|---|
| Methods_comparison_Promega_raw_data.zip Zip file containing raw sequencing data for samples extracted with Promega kit (FASTQ) and MIMARKS-compliant sampling metadata (.xlsx, .csv) |
coral_microbiome_methods_ comp_FGDC_metadata.xml |
coral_microbiome_methods_ comp_FGDC_metadata.txt |
Methods_comparison_ Promega_raw_data.zip (571.8 MB) |
| Methods_comparison_Qiagen_raw_data.zip Zip file containing raw sequencing data for samples extracted with Qiagen kit (FASTQ) and MIMARKS-compliant sampling metadata (.xlsx, .csv) |
Same as above | Same as above | Methods_comparison_ Qiagen_raw_data.zip (577.8 MB) |
| Supplemental information | |||
| README_Methods_comp.txt Readme file explaining data |
Not applicable | Not applicable | README_Methods_comp.txt (5 KB) |
Figure 1. Locations of three sampling areas.
Suggested Citation
Kellogg, C.A., Goldsmith, D.B., and Voelschow, J.J., 2021, Coral microbiome preservation and extraction method comparison—raw data: U.S. Geological Survey data release, https://doi.org/10.5066/P96GBWDM.