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Cold-water coral microbiomes (Astrangia poculata) from Narragansett Bay: sequence data

Metadata Updated: July 6, 2024

The files provided in this data release are the DNA sequence files referenced in Goldsmith and others (2019), which represent a 16S ribosomal ribonucleic acid (rRNA) gene amplicon survey of Astrangia poculata microbiomes completed using Sanger dideoxy sequencing. The coral samples were collected from Narragansett Bay at Fort Wetherill State Park, Jamestown, Rhode Island in 2015 and 2016 (Sharp and others, 2017). Sequences were obtained by first extracting DNA from a fragment of each A. poculata sample comprising mucus, tissue, and skeleton. Bacterial DNA was amplified from all samples by polymerase chain reaction (PCR), using primers 8F (5’–AGA GTT TGA TCC TGG CTC AG) and 1492R (5’–GGT TAC CTT GTT ACG ACT T) to target the 16S rDNA gene in bacteria. Archaeal DNA from two of the samples (FW1B8 and FW1W8) was amplified using primers 21F (5'–TTC CGG TTG ATC CYG CCG GA) and 958R (5'–YCC GGC GTT GAM TCC AAT T) to target the 16S rDNA gene from archaea. All amplicons were visualized on an agarose gel, extracted from the gel, quantitated, cloned into a vector, and used to transform competent cells. Inserts in positive transformants were sequenced by the Clemson University Genomics Computational Laboratory (Clemson, SC). The sequences were processed by trimming vectors and ends, removing sequences less than 50 base pairs (bp), checking for chimeras, classifying taxonomy, and removing unclassified, chloroplast, and mitochondrial sequences. After processing, 806 bacterial operational taxonomic units (OTUs) and 18 archaeal OTUs remained. Sequences representing each OTU have been deposited in the National Center for Biotechnology Information’s (NCBI) GenBank archive, and have been assigned accession numbers MK175495 through MK176300 (bacterial sequences) and MH915525 through MH915542 (archaeal sequences). Minimum information about a marker gene (MIMARKS) compliant metadata files are also included in the data download files. For more information, please contact Christina Kellogg at the U.S. Geological Survey (USGS) St. Petersburg Coastal and Marine Science Center, 600 4th Street South, St. Petersburg, Florida, USA, 33701; Telephone: (727) 502-8128; Email: ckellogg@usgs.gov.

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 June 1, 2023
Metadata Updated Date July 6, 2024

Metadata Source

Harvested from DOI EDI

Additional Metadata

Resource Type Dataset
Metadata Created Date June 1, 2023
Metadata Updated Date July 6, 2024
Publisher U.S. Geological Survey
Maintainer
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Identifier USGS:e78e6690-fcf4-405a-8db4-d839f4f0fb37
Data Last Modified 20201013
Category geospatial
Public Access Level public
Bureau Code 010:12
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Metadata Catalog ID https://datainventory.doi.gov/data.json
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Metadata Type geospatial
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Publisher Hierarchy White House > U.S. Department of the Interior > U.S. Geological Survey
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