http://lod.bco-dmo.org/id/dataset/986592 eng; USA utf8 dataset Highest level of data collection, from a common set of sensors or instrumentation, usually within the same research project Biological and Chemical Oceanography Data Management Office (BCO-DMO) Unavailable 508-289-2009 WHOI MS#36 Woods Hole MA 02543 USA info@bco-dmo.org http://www.bco-dmo.org Monday - Friday 8:00am - 5:00pm For questions regarding this resource, please contact BCO-DMO via the email address provided. pointOfContact 2025-10-13 ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data ISO 19115-2:2009(E) NCBI Sequence Read Archive (SRA) accession numbers for fastq sequence files of 16S amplicons from a longitudinal study of SCTLD at St. John, U.S. Virgin Islands from 2020 to 2024 2025-11-18 publication 2025-11-18 revision Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA) 2025-11-19 publication https://doi.org/10.26008/1912/bco-dmo.986592.1 Amy Apprill Woods Hole Oceanographic Institution principalInvestigator Marilyn Brandt University of the Virgin Islands Center for Marine and Environmental Studies principalInvestigator Biological and Chemical Oceanography Data Management Office (BCO-DMO) Unavailable 508-289-2009 WHOI MS#36 Woods Hole MA 02543 USA info@bco-dmo.org http://www.bco-dmo.org Monday - Friday 8:00am - 5:00pm For questions regarding this resource, please contact BCO-DMO via the email address provided. publisher Cite this dataset as: Bloomberg, J., Apprill, A., Brandt, M., Becker, C. C., Meiling, S. (2025) NCBI Sequence Read Archive (SRA) accession numbers for fastq sequence files of 16S amplicons from a longitudinal study of SCTLD at St. John, U.S. Virgin Islands from 2020 to 2024. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2025-11-18 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.986592.1 [access date] Longitudinal study NCBI SRA Dataset Description: Methods and Sampling: &lt;p&gt;Samples were collected on day-trips aboard a University of the Virgin Islands powerboat in the U.S. Virgin Islands from July 2020 through March 2024. On SCUBA, 60 milliliters (mL) of seawater was collected 2-5 centimeters (cm) above the colony surface, then the coral fragment was collected; upon surfacing, samples were put on ice. Seawater was passed through 0.2-micrometer (µm) filters, and the tissue was removed from the skeleton using PBS solution and an airbrush. DNA was extracted from the coral tissue, seawater filters, and processing controls using the Qiagen DNeasy PowerBiofilm Kit. PCR was used to amplify the V4 region of the small subunit rRNA gene of bacteria and archaea using primers 515FY and 806RB with standard barcodes. To purify the PCR product from seawater, the Qiagen PCR Purification Kit was used. Purification of PCR products from coral tissue proceeded by running products in a 1.5% agarose gel and excising bands of 450 bp. Gel excisions were purified using the Qiagen Gel Extraction Kit. PCR products were diluted to 1 nanogram per microliter (ng/μL) and sequenced on an Illumina MiSeq (paired reads, 2x250 nt) at the University of Georgia's Georgia Genomics and Bioinformatics Core and University of Illinois Urbana-Champaign's Roy J. Carver Biotechnology Center.&lt;/p&gt; Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-2109622 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=2109622 completed Amy Apprill Woods Hole Oceanographic Institution 508-289-2649 Marine Chemistry and Geochemistry Department 266 Woods Hole Road, MS# 4 Woods Hole MA 02543 USA aapprill@whoi.edu pointOfContact Marilyn Brandt University of the Virgin Islands Center for Marine and Environmental Studies 340-693-1379 2 John Brewers Bay St. Thomas, USVI 00802 mbrandt@uvi.edu pointOfContact asNeeded Dataset Version: 1 Unknown Experiment_Accession Instrument Study_Accession Study_Title Sample_Accession Library_Name Collection_date Latitude Longitude agarose gel Illumina MiSeq V2 SCUBA PCR theme None, User defined NCBI SRA experiment accession (SRX) instrument NCBI SRA study accession (SRP) brief description NCBI SRA Sample accession (SRS) sample identification date latitude longitude featureType BCO-DMO Standard Parameters Agarose Gel Electrophoresis System Automated DNA Sequencer Self-Contained Underwater Breathing Apparatus Thermal Cycler instrument BCO-DMO Standard Instruments otherRestrictions otherRestrictions Access Constraints: none. Use Constraints: Please follow guidelines at: http://www.bco-dmo.org/terms-use Distribution liability: Under no circumstances shall BCO-DMO be liable for any direct, incidental, special, consequential, indirect, or punitive damages that result from the use of, or the inability to use, the materials in this data submission. If you are dissatisfied with any materials in this data submission your sole and exclusive remedy is to discontinue use. A multi-scale approach to predicting infectious multi-host disease spread in marine benthic communities https://osprey.bco-dmo.org/project/877263 A multi-scale approach to predicting infectious multi-host disease spread in marine benthic communities <p><em>NSF Award Abstract:</em><br /> Marine diseases have devastating impacts on ocean ecosystems and this work will directly examine the framework for understanding disease transmission in the ocean. A team of ecologists, ocean connectivity and disease modelers, microbiologists, and coral immunologists (from the University of Virgin Islands (UVI), Louisiana State University (LSU), Rice University, University of Texas-Arlington and the Woods Hole Oceanographic Institution) will develop a model that predicts transmission of a devastating Caribbean coral disease that has the potential to impact the economic value of coral reefs, including those located in the U.S. This project will support multidisciplinary field and laboratory research experiences of graduate students at multiple minority-serving institutions, and will provide undergraduate students with hands-on training in modeling, ecological and molecular analysis techniques. UVI and LSU are in EPSCoR jurisdictions and have diverse student bodies, including numerous under-represented minority (URM) students. The research team will collaboratively provide URM students with research experiences in STEM fields. Project findings will be broadly communicated through virtual public programming, and through the Virgin Islands Coral Disease Advisory Committee with updates on the vicoraldisease.org website. A coral disease response workshop for the U.S. Virgin Islands will also be held, in which project results will be presented and used to support disease response planning.</p> <p>Over the last four decades, marine diseases have decimated ecosystem engineers in marine coastal ecosystems, including the rocky intertidal, seagrasses and coral reefs. The pathogens driving these diseases have frequently been challenging to isolate, characterize and confirm, in part because they affect multiple host species and can spread by ocean currents, as well as through individual contact. Here, we propose a multi-scale epidemic model for studying marine disease that addresses both within-host and within-patch disease dynamics, and explicitly acknowledges the dispersal of pathogens between populations. Our interdisciplinary research team of ecologists, connectivity and disease modelers, microbiologists, and coral immunologists will integrate the largest set of predictors of marine disease spread to date: individual host species traits that allow for disease resistance or susceptibility, local transmission within communities that may have unique community structure, and hydrodynamic connectivity among susceptible communities. Modeling will be supported with rich data sets of within- and among-patch population characteristics and disease dynamics as well as molecular data on species-level disease responses. This project will advance knowledge of infectious diseases by integrating multidimensional scales and differential host susceptibilities into existing epidemiological models. This model will particularly advance the framework for studying marine diseases and has the potential to elucidate the transmission properties of a devastating Caribbean coral disease (stony coral tissue loss disease) that fits the most confounding and notorious hallmarks of marine diseases: infection of multiple hosts by an elusive pathogen.</p> <p>This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.</p> Multi-scale multi-host disease spread largerWorkCitation project eng; USA oceans -64.7642 -64.704017 18.31462 18.337967 2020-07-16 2024-03-07 United States Virgin Islands 0 BCO-DMO catalogue of parameters from NCBI Sequence Read Archive (SRA) accession numbers for fastq sequence files of 16S amplicons from a longitudinal study of SCTLD at St. John, U.S. Virgin Islands from 2020 to 2024 Biological and Chemical Oceanography Data Management Office (BCO-DMO) Unavailable 508-289-2009 WHOI MS#36 Woods Hole MA 02543 USA info@bco-dmo.org http://www.bco-dmo.org Monday - Friday 8:00am - 5:00pm For questions regarding this resource, please contact BCO-DMO via the email address provided. pointOfContact http://lod.bco-dmo.org/id/dataset-parameter/988130.rdf Name: Experiment_Accession Units: unitless Description: <p>NCBI experiment accession number</p> http://lod.bco-dmo.org/id/dataset-parameter/988131.rdf Name: Instrument Units: unitless Description: <p>Sequencing instrument used</p> http://lod.bco-dmo.org/id/dataset-parameter/988132.rdf Name: Study_Accession Units: unitless Description: <p>NCBI study accession number</p> http://lod.bco-dmo.org/id/dataset-parameter/988133.rdf Name: Study_Title Units: unitless Description: <p>Title of study on NCBI</p> http://lod.bco-dmo.org/id/dataset-parameter/988134.rdf Name: Sample_Accession Units: unitless Description: <p>NCBI sample accession number</p> http://lod.bco-dmo.org/id/dataset-parameter/988135.rdf Name: Library_Name Units: unitless Description: <p>Sample name used during the experiment</p> http://lod.bco-dmo.org/id/dataset-parameter/988999.rdf Name: Collection_date Units: unitless Description: <p>Date that the sample was collected from reef site</p> http://lod.bco-dmo.org/id/dataset-parameter/989000.rdf Name: Latitude Units: decimal degrees Description: <p>Latitude of reef site</p> http://lod.bco-dmo.org/id/dataset-parameter/989002.rdf Name: Longitude Units: decimal degrees Description: <p>Latitude of reef site</p> GB/NERC/BODC > British Oceanographic Data Centre, Natural Environment Research Council, United Kingdom Biological and Chemical Oceanography Data Management Office (BCO-DMO) Unavailable 508-289-2009 WHOI MS#36 Woods Hole MA 02543 USA info@bco-dmo.org http://www.bco-dmo.org Monday - Friday 8:00am - 5:00pm For questions regarding this resource, please contact BCO-DMO via the email address provided. pointOfContact 37273 https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/fbdedea9-1907-4d49-a0c8-3ef19337795e/content download https://doi.org/10.26008/1912/bco-dmo.986592.1 download onLine dataset &lt;p&gt;Samples were collected on day-trips aboard a University of the Virgin Islands powerboat in the U.S. Virgin Islands from July 2020 through March 2024. On SCUBA, 60 milliliters (mL) of seawater was collected 2-5 centimeters (cm) above the colony surface, then the coral fragment was collected; upon surfacing, samples were put on ice. Seawater was passed through 0.2-micrometer (µm) filters, and the tissue was removed from the skeleton using PBS solution and an airbrush. DNA was extracted from the coral tissue, seawater filters, and processing controls using the Qiagen DNeasy PowerBiofilm Kit. PCR was used to amplify the V4 region of the small subunit rRNA gene of bacteria and archaea using primers 515FY and 806RB with standard barcodes. To purify the PCR product from seawater, the Qiagen PCR Purification Kit was used. Purification of PCR products from coral tissue proceeded by running products in a 1.5% agarose gel and excising bands of 450 bp. Gel excisions were purified using the Qiagen Gel Extraction Kit. PCR products were diluted to 1 nanogram per microliter (ng/μL) and sequenced on an Illumina MiSeq (paired reads, 2x250 nt) at the University of Georgia's Georgia Genomics and Bioinformatics Core and University of Illinois Urbana-Champaign's Roy J. Carver Biotechnology Center.&lt;/p&gt; Specified by the Principal Investigator(s) - Imported original file &quot;sra_result.csv&quot; into the BCO-DMO system. - Renamed fields to comply with BCO-DMO naming conventions. - Saved the final file as &quot;986592_v1_ncbi_sra.csv&quot;. Specified by BCO-DMO Data Managers asNeeded 7.x-1.1 Biological and Chemical Oceanography Data Management Office (BCO-DMO) Unavailable 508-289-2009 WHOI MS#36 Woods Hole MA 02543 USA info@bco-dmo.org http://www.bco-dmo.org Monday - Friday 8:00am - 5:00pm For questions regarding this resource, please contact BCO-DMO via the email address provided. pointOfContact agarose gel agarose gel PI Supplied Instrument Name: agarose gel PI Supplied Instrument Description:Purification of PCR products from coral tissue proceeded by running products in a 1.5% agarose gel and excising bands of 450 bp. Instrument Name: Agarose Gel Electrophoresis System Instrument Short Name:agarose gel electrophoresis system Instrument Description: A gel electrophoresis system that is used to separate DNA or RNA molecules by size, achieved by moving negatively charged nucleic acid molecules through an agarose matrix with an electric field. Illumina MiSeq V2 Illumina MiSeq V2 PI Supplied Instrument Name: Illumina MiSeq V2 PI Supplied Instrument Description:Samples were sequenced on an Illumina MiSeq V2. Instrument Name: Automated DNA Sequencer Instrument Short Name:Automated Sequencer Instrument Description: A DNA sequencer is an instrument that determines the order of deoxynucleotides in deoxyribonucleic acid sequences. SCUBA SCUBA PI Supplied Instrument Name: SCUBA PI Supplied Instrument Description:Samples were collected by SCUBA divers. Instrument Name: Self-Contained Underwater Breathing Apparatus Instrument Short Name:SCUBA Instrument Description: The self-contained underwater breathing apparatus or scuba diving system is the result of technological developments and innovations that began almost 300 years ago. Scuba diving is the most extensively used system for breathing underwater by recreational divers throughout the world and in various forms is also widely used to perform underwater work for military, scientific, and commercial purposes. Reference: https://oceanexplorer.noaa.gov/technology/technical/technical.html PCR PCR PI Supplied Instrument Name: PCR PI Supplied Instrument Description:PCR was used to amplify the V4 region of the small subunit rRNA gene of bacteria and archaea using primers 515FY and 806RB with standard barcodes. Instrument Name: Thermal Cycler Instrument Short Name:Thermal Cycler Instrument Description: A thermal cycler or "thermocycler" is a general term for a type of laboratory apparatus, commonly used for performing polymerase chain reaction (PCR), that is capable of repeatedly altering and maintaining specific temperatures for defined periods of time. The device has a thermal block with holes where tubes with the PCR reaction mixtures can be inserted. The cycler then raises and lowers the temperature of the block in discrete, pre-programmed steps. They can also be used to facilitate other temperature-sensitive reactions, including restriction enzyme digestion or rapid diagnostics. (adapted from http://serc.carleton.edu/microbelife/research_methods/genomics/pcr.html)