Cold-water coral microbiomes (Anthothela spp.) from Baltimore and Norfolk Canyons: raw and processed data

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Frequently anticipated questions:

What does this data set describe?

Title:
Cold-water coral microbiomes (Anthothela spp.) from Baltimore and Norfolk Canyons: raw and processed data
Abstract:
The files included in this data release are the raw and processed deoxyribonucleic acid (DNA) sequence files referenced in the journal article by Lawler and others (2016) entitled “Coral-Associated Bacterial Diversity is Conserved Across Two Deep-Sea Anthothela Species”. They represent a 16S rRNA gene amplicon survey of cold-water corals (Anthothela spp.) microbiomes completed using Roche 454 pyrosequencing with titanium reagents. The samples used in this study were collected from cold-water corals between 2012-2013, at Baltimore and Norfolk Canyons in the Atlantic Ocean. The raw data files associated with this study were also submitted to the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA), under Bioproject number PRJNA296835.
Supplemental_Information:
Coral samples were collected under Field Activity Number (FAN) 12DCM02 and 13DCM01. FANs are unique identifiers assigned by the U.S. Geological Survey (USGS) to provide more information about the activities conducted in the field for a study. Please visit the Coastal and Marine Geoscience Data System (CMGDS) field activity webpage for more information about each FAN related to this dataset, https://cmgds.marine.usgs.gov/fan_info.php?fan=12DCM02 and https://cmgds.marine.usgs.gov/fan_info.php?fan=13DCM01.
  1. How might this data set be cited?
    Kellogg, Christina A., and Voelschow, Julie J., 20220418, Cold-water coral microbiomes (Anthothela spp.) from Baltimore and Norfolk Canyons: raw and processed data:.

    This is part of the following larger work.

    Kellogg, Christina A., and Lawler, Stephanie N., 20151211, Cold-water coral microbiomes (Anthothela spp.) from Baltimore and Norfolk Canyons: raw and processed data: U.S. Geological Survey data release doi:10.5066/F7CZ356K, U.S. Geological Survey - St. Petersburg Coastal and Marine Science Center, St. Petersburg, Florida.

    Online Links:

  2. What geographic area does the data set cover?
    West_Bounding_Coordinate: -74.605852
    East_Bounding_Coordinate: -73.834483
    North_Bounding_Coordinate: 38.181985
    South_Bounding_Coordinate: 37.023429
  3. What does it look like?
  4. Does the data set describe conditions during a particular time period?
    Beginning_Date: 10-Sep-2012
    Ending_Date: 20-May-2013
    Currentness_Reference:
    ground condition
  5. What is the general form of this data set?
    Geospatial_Data_Presentation_Form:
    SFF files, QUAL files, FNA files (FASTA files), and tabular digital data
  6. How does the data set represent geographic features?
    1. How are geographic features stored in the data set?
    2. What coordinate system is used to represent geographic features?
  7. How does the data set describe geographic features?
    Entity_and_Attribute_Overview:
    Please refer to the "README" file, README.txt, for detailed descriptions of the contents of the Anthothela raw data files and the processed data files. Additional information is contained in the metadata file, anthothela_metadata.txt, which is also included in the raw_data.zip downloadable file of this data release (Kellogg and Lawler, 2015).
    Entity_and_Attribute_Detail_Citation:
    The entity and attribute information were generated by the individual and/or agency identified as the originator of the dataset. Please review the rest of the metadata record for additional details and information.

Who produced the data set?

  1. Who are the originators of the data set? (may include formal authors, digital compilers, and editors)
    • Christina A. Kellogg
    • Julie J. Voelschow
  2. Who also contributed to the data set?
  3. To whom should users address questions about the data?
    Christina A. Kellogg
    U.S. Geological Survey
    Research Microbiologist
    600 4th St. South
    St. Petersburg, Florida
    United States

    727-502-8128 (voice)
    ckellogg@usgs.gov

Why was the data set created?

This experiment was conducted to explore the diversity and abundance of microbial associates in Anthothela species.

How was the data set created?

  1. From what previous works were the data drawn?
  2. How were the data generated, processed, and modified?
    Date: 20-May-2013 (process 1 of 4)
    Coral collection: Twenty-three Anthothelidae colonies were sampled using remotely-operated vehicles during two separate cruises (August 2012 and May 2013) from Baltimore Canyon and Norfolk Canyon, in the Mid-Atlantic ocean. Coral samples were preserved in sterile 50 milliliter (mL) tubes and stored overnight in RNAlater at 4 degrees Celsius (˚C) before extended storage at -20˚C.
    Date: 24-Jul-2013 (process 2 of 4)
    DNA extraction: DNA was extracted in July 2013, using MOBIO PowerPlant DNA Isolation Kit (now Qiagen), with modifications per the Sunagawa lab protocol (2010), including the addition of lysozyme and extended incubation periods at room temperature (~21˚C), 24˚C, and 65˚C.
    Date: 13-Aug-2013 (process 3 of 4)
    DNA sequencing: In August 2013, a 16S rRNA gene amplicon survey of the corals microbiomes was completed by Selah Genomics (Greenville, SC), using Roche 454 pyrosequencing with titanium reagents, using primers targeting the V4-V5 hypervariable region of the16S rRNA gene (563F/926R); V4-forward: 5’-AYTGGGYDTAAAGNG and V5-reverse: 5’ CGTATCGCCTCCCTCGCGCCATCAG.
    Date: 01-Sep-2015 (process 4 of 4)
    Data analysis: Sequence data were analyzed using the bioinformatic packages Quantitative Insights Into Microbial Ecology (QIIME) version 1.5.0 and QIIME 1.9.1 packages (Caporaso and others, 2010). Please refer to the file entitled “Anthothela_workflow.txt," which is included as a supplemental file in the processed_data.zip package and details the scripts run in QIIME. The workflow file contains the default or chosen settings used for each script, as well as the names of the input/output files associated with each script.
  3. What similar or related data should the user be aware of?
    Mo BIO Laboratories, Inc., 20130816, MO BIO's PowerPlant DNA Isolation Kit Handbook.

    Online Links:

    Sunagawa, Shinichi, Woodley, Cheryl M., and Medina, Monica, 20100305, Threatened Corals Provide Underexplored Microbial Habitats: PLOS One Volume 5, Number 3.

    Online Links:

    Lawler, Stephanie N., Kellogg, Christina A., France, Scott C., Clostio, Rachel W., Brooke, Sandra D., and Ross, Steve W., 20160405, Coral-Associated Bacterial Diversity is Conserved Across Two Deep-Sea Anthothela Species: Frontiers in Microbiology Volume 7.

    Online Links:

    Caporaso, Gregory J., Kuczynski, Justin, Stombaugh, Jesse, Bittinger, Kyle, Bushman, Frederic D., Costello, Elizabeth K., Fierer, Noah, Pena, Antonio Gonzalez, Goodrich, Julie K., Gordon, Jeffrey I., Huttley, Gavin A., Kelley, Scott T., Knights, Dan, Koenig, Jeremy E., Ley, Ruth E., Lozupone, Catherine A., McDonald, Daniel, Muegge, Brian D., Oirrung, Meg, Reeder, Jens, Sevinsky, Joel R., Tumbaugh, Peter J., Walters, William A., Widmann, Jeremy, Yatzunenko, Tanya, Zaneveld, Jesse, and Knight, Rob, 20100501, QIIME allows analysis of high-throughput community sequencing data: Nature Methods 7(5): 335–336.

    Online Links:

How reliable are the data; what problems remain in the data set?

  1. How well have the observations been checked?
    No formal attribute accuracy tests were conducted.
  2. How accurate are the geographic locations?
  3. How accurate are the heights or depths?
  4. Where are the gaps in the data? What is missing?
    Dataset is considered complete for the information presented, as described in the abstract.
  5. How consistent are the relationships among the observations, including topology?
    No formal logical accuracy tests were conducted.

How can someone get a copy of the data set?

Are there legal restrictions on access or use of the data?
Access_Constraints None. Please see 'Distribution Info' for details.
Use_Constraints None. Users are advised to read the dataset's metadata thoroughly to understand appropriate use and data limitations.
  1. Who distributes the data set? (Distributor 1 of 1)
    Christina A. Kellogg
    U.S. Geological Survey
    Research Microbiologist
    600 4th St. South
    St. Petersburg, Florida
    United States

    727-502-8128 (voice)
    ckellogg@usgs.gov
  2. What's the catalog number I need to order this data set?
  3. What legal disclaimers am I supposed to read?
    Unless otherwise stated, all data, metadata and related materials are considered to satisfy the quality standards relative to the purpose for which the data were collected. Although these data and associated metadata have been reviewed for accuracy and completeness and approved for release by the U.S. Geological Survey (USGS), no warranty expressed or implied is made regarding the display or utility of the data on any other system or for general or scientific purposes, nor shall the act of distribution constitute any such warranty.
  4. How can I download or order the data?

Who wrote the metadata?

Dates:
Last modified: 15-May-2023
Metadata author:
Christina A. Kellogg
U.S. Geological Survey
Research Microbiologist
600 4th St. South
St. Petersburg, Florida
United States

727-502-8128 (voice)
ckellogg@usgs.gov
Metadata standard:
FGDC Biological Data Profile of the Content Standard for Digital Geospatial Metadata (FGDC-STD-001.1-1999)
This page is <https://cmgds.marine.usgs.gov/catalog/spcmsc/Anthothela_BaltimoreNorfolk_FGDC_metadata.faq.html>
Generated by mp version 2.9.51 on Mon May 15 10:13:53 2023