http://lod.bco-dmo.org/id/dataset/985619 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 2025-10-01 ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data ISO 19115-2:2009(E) Transcriptome and viral metagenome data from Diadema antillarum collected at St. Thomas (USVI) and Saba (Caribbean Netherlands) in Apr 2022 2025-10-07 publication 2025-10-07 revision Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA) 2025-10-07 publication https://doi.org/10.26008/1912/bco-dmo.985619.1 Ian Hewson Cornell University principalInvestigator Marilyn Brandt University of the Virgin Islands Center for Marine and Environmental Studies principalInvestigator Mya Breitbart University of South Florida principalInvestigator Michael Henson Northern Illinois University principalInvestigator Alwin Hylkema Van Hall Larenstein University of Applied Sciences 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: Hewson, I., Brandt, M., Budd, K., Breitbart, M., DeRito, C., Gittens, S., Henson, M., Hylkema, A., Sevier, M., Souza, M., Vilanova-Cuevas, B., Von Hoene, S. (2025) Transcriptome and viral metagenome data from Diadema antillarum collected at St. Thomas (USVI) and Saba (Caribbean Netherlands) in Apr 2022. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2025-10-07 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.985619.1 [access date] Diadema antillarum transcriptomes Dataset Description: Methods and Sampling: &lt;p&gt;&lt;strong&gt;Collection&lt;/strong&gt;&lt;/p&gt; &lt;p&gt;Specimens of&amp;nbsp;&lt;em&gt;Diadema antillarum&lt;/em&gt; (urn:lsid:marinespecies.org:taxname:124332)&amp;nbsp; were collected by snorkel and transported to the lab in seawater buckets. The specimens were photographed, and vivisected into tissue components (body wall, spine, gonad, digestive tract and coelomic fluid), which were then frozen in liquid N2 for transport to the laboratory at Cornell University.&amp;nbsp;&lt;/p&gt; &lt;p&gt;&lt;strong&gt;Transcriptomic Sequencing&amp;nbsp;&lt;/strong&gt;&lt;/p&gt; &lt;p&gt;Transcriptomes from coelomic fluid of grossly normal (&lt;em&gt;n&lt;/em&gt;&amp;nbsp;=&amp;nbsp;2) and abnormal (&lt;em&gt;n&lt;/em&gt;&amp;nbsp;=&amp;nbsp;2) individuals from an affected site and of grossly normal individuals from a reference site (&lt;em&gt;n&lt;/em&gt;&amp;nbsp;=&amp;nbsp;2) were prepared alongside grossly normal (&lt;em&gt;n&lt;/em&gt;&amp;nbsp;=&amp;nbsp;2) aboral body wall tissues from a reference site to examine expressed genes and microorganisms associated with infection. RNA was extracted from coelomic fluid (300&amp;nbsp;μl) and body wall tissues (200 mg) using the Zymo Quick-RNA Tissue/Insect Kit using on-column deoxyribonuclease I digestion per the manufacturer’s protocols. Transcriptome libraries were prepared from purified RNA extracts using the Zymo RiboFree kit and sequenced on a single run of Illumina MiSeq using a Nextera DNA Library Prep Kit at the Biotechnology Resource Center at Cornell University. All sequences have been deposited at National Center for Biotechnology Information (NCBI) Sequence Read Archive under Bioproject&amp;nbsp;PRJNA900371 and SRA&amp;nbsp;accession numbers SRR22260770 to SRR22260777.&lt;/p&gt; &lt;p&gt;&lt;strong&gt;Viral Metagenomic Sequencing&lt;/strong&gt;&lt;/p&gt; &lt;p&gt;Small subsamples of each specimen were prepared for viral metagenomic sequencing broadly following the approach of Ng et al. (2011). Briefly, tissues were homogenized in sterile, 0.02&amp;nbsp;µm filtered phosphate buffered saline by beating using Zymo ZR Basher Beads (part number S6012-50) in a Biospec Instruments homogenizer for 1 min at maximum speed. The homogenates were centrifuged at 3,000 × g for 1 min to remove large cell debris, before filtering the supernatant through 0.2&amp;nbsp;µm pore size polyethersulfone syringe filters. Filtered homogenates were treated with 5U Turbo DNase (Invitrogen; part number AM2238), 5U Benzonase nuclease (Sigma Aldrich; part number E1014) and 20U RNase ONE (Promega; part number M4261) for 2 hours at 37&amp;nbsp;°C to digest extracellular and non-ribosome-bound nucleic acids. Following incubation, RNA was extracted from subsamples of purified virus-sized material using the Zymo Viral RNA kit (part number R1034) before storing RNA at −80&amp;nbsp;°C until further processing.&lt;/p&gt; &lt;p&gt;RNA in viral extracts was amplified using the SeqPlex RNA kit (Sigma Aldrich; part number SEQXE-10RXN, &lt;em&gt;n&lt;/em&gt;&amp;nbsp;=&amp;nbsp;11 libraries). Subsequent specimens were amplified using the TransPlex kit (WTA2; Sigma Aldrich; part number WTA2-10RXN, &lt;em&gt;n&lt;/em&gt;&amp;nbsp;=&amp;nbsp;3 libraries), which was used in prior RNA viral metagenomic work. Amplification products were purified using the Zymo DNA Clean and Concentrator -5 (part number D4004), quantified by Pico Green fluorescence (Invitrogen; part number P11496), and submitted for sequencing at the Cornell Biotechnology Resource Center. Libraries were prepared for sequencing using the Nextera Flex kit (Illumina; part number 20018704) and sequenced on the Illumina MiSeq platform using the 500 bp Nano kit. Sequences from all libraries were archived at NCBI under Bioproject PRJNA1117494 and SRA accessions SRR29258987 to SRR29258999.&lt;/p&gt; Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-2049225 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=2049225 completed Ian Hewson Cornell University 1-607-255-0151 Department of Microbiology Wing Hall 403 Ithaca NY 14853 USA hewson@cornell.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 Mya Breitbart University of South Florida (727) 553-3520 USF College of Marine Sciences 140 7th Avenue South St Petersburg FL 33701 USA mya@marine.usf.edu pointOfContact Michael Henson Northern Illinois University mhenson@niu.edu pointOfContact Alwin Hylkema Van Hall Larenstein University of Applied Sciences alwin.hylkema@hvhl.nl pointOfContact asNeeded Dataset Version: 1 Unknown SRA_accession SRA_study bioproject_accession biosample_accession sample_name library_ID title library_strategy library_source library_selection library_layout platform instrument_model design_description filetype Latitude Longitude Date_specimen_collected Illumina MiSeq Photographed Centrifuge Snorkel Biospec Instruments homogenizer Incubator theme None, User defined NCBI SRA run accession (SRR) NCBI SRA study accession (SRP) NCBI BioProject accession NCBI BioSample accession sample identification seq_descrip instrument instrument model datatype latitude longitude date featureType BCO-DMO Standard Parameters Automated DNA Sequencer Camera Centrifuge Diving Mask and Snorkel Homogenizer Incubator 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. Exploring the role of boundary layer microbial remineralization in flavivirus-host dynamics https://osprey.bco-dmo.org/project/863960 Exploring the role of boundary layer microbial remineralization in flavivirus-host dynamics <p>NSF Award Abstract:</p> <p>Marine diseases pose considerable risks to invertebrates, such as sea cucumbers, in the face of changing ocean conditions. While many invertebrate diseases are driven by pathogens, the interplay between animal biology and environmental conditions often mediates the outcome of the pathogen-host relationship. Sea cucumbers are ecologically and economically important animals that occur in a wide range of marine habitats. This project aims to decipher how the interaction between the biology of sea cucumbers, environmental conditions, and a newly-discovered type of virus, seemingly innocuous under typical conditions, may lead to lethal disease in giant Pacific sea cucumbers in the U.S. West Coast. The study includes surveys in coastal regions in southeast Alaska, Washington, and California as well as laboratory experiments manipulating seawater oxygen concentrations, temperature, and simulated microalgal blooms. The project engages community scientists, fishers, high school students, and indigenous groups, and supports training of one graduate and several undergraduate students. A workshop that brings together scientists across marine ecology, disease, and veterinary disciplines is planned to prepare a handbook of best practices in marine disease investigation.</p> <p>Metagenomic and community-level sequencing efforts have revealed an astonishing diversity of viruses associated with grossly normal marine invertebrates. The vast majority of detected viruses likely represents asymptomatic infections under typical conditions but may generate pathology in hosts under changing environmental conditions. This project investigates the ecology of a group of enveloped positive sense single-stranded RNA viruses (flaviviruses) that this research team has recently discovered in the giant California sea cucumber Apostichopus californicus by addressing three hypotheses: 1) Aquatic insect-only Flaviviruses (aiFVs) do not cause gross pathology under typical conditions; 2) aiFVs proliferate and generate clinical and gross pathology under suboxic stress; and 3) Periodic increases in primary production and mean temperature excursions cause aiFV proliferation and subsequently exacerbate holothurian disease process. The study comprises a restricted survey of aiFV diversity via amplicon sequencing and their prevalence within and between populations, development of an antibody-based approach for aiFV detection, and examination of aiFV behavior in concert with host transcription and veterinary pathology. The study includes field surveys and in laboratory manipulative experiments.</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> Holothurian Flaviviruses largerWorkCitation project eng; USA biota oceans -64.694 -63.2181 17.616 18.3451 2022-04-07 2022-04-21 Northeastern Pacific Ocean 0 BCO-DMO catalogue of parameters from Transcriptome and viral metagenome data from Diadema antillarum collected at St. Thomas (USVI) and Saba (Caribbean Netherlands) in Apr 2022 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/985631.rdf Name: SRA_accession Units: unitless Description: <p>NCBI Run accession in the Sequence Read Archive (SRA)</p> http://lod.bco-dmo.org/id/dataset-parameter/985632.rdf Name: SRA_study Units: unitless Description: <p>NCBI study accession in the Sequence Read Archive (SRA)</p> http://lod.bco-dmo.org/id/dataset-parameter/985634.rdf Name: bioproject_accession Units: unitless Description: <p>NCBI BioProject identifier</p> http://lod.bco-dmo.org/id/dataset-parameter/985635.rdf Name: biosample_accession Units: unitless Description: <p>NCBI BioSample accession number</p> http://lod.bco-dmo.org/id/dataset-parameter/985636.rdf Name: sample_name Units: unitless Description: <p>Sample Name of Initial Sample</p> http://lod.bco-dmo.org/id/dataset-parameter/985637.rdf Name: library_ID Units: unitless Description: <p>Library Name of Sequence Data</p> http://lod.bco-dmo.org/id/dataset-parameter/985638.rdf Name: title Units: unitless Description: <p>NCBI Identifier Description</p> http://lod.bco-dmo.org/id/dataset-parameter/985639.rdf Name: library_strategy Units: unitless Description: <p>Sequencing library strategy: RNA-Seq</p> http://lod.bco-dmo.org/id/dataset-parameter/985640.rdf Name: library_source Units: unitless Description: <p>Source of sequencing library: Transcriptome or Metagenome</p> http://lod.bco-dmo.org/id/dataset-parameter/985641.rdf Name: library_selection Units: unitless Description: <p>How libraries were prepared for sequencing: size selected or random</p> http://lod.bco-dmo.org/id/dataset-parameter/985642.rdf Name: library_layout Units: unitless Description: <p>Description of sequencing reads: paired</p> http://lod.bco-dmo.org/id/dataset-parameter/985643.rdf Name: platform Units: unitless Description: <p>Sequencing Platform</p> http://lod.bco-dmo.org/id/dataset-parameter/985644.rdf Name: instrument_model Units: unitless Description: <p>Sequencing Instrument Used</p> http://lod.bco-dmo.org/id/dataset-parameter/985645.rdf Name: design_description Units: unitless Description: <p>Brief description of how libraries were prepared from source material</p> http://lod.bco-dmo.org/id/dataset-parameter/985646.rdf Name: filetype Units: unitless Description: <p>Sequence file format</p> http://lod.bco-dmo.org/id/dataset-parameter/985647.rdf Name: Latitude Units: decimal degrees Description: <p>Latitude the specimens were collected, North is positive</p> http://lod.bco-dmo.org/id/dataset-parameter/985649.rdf Name: Longitude Units: decimal degrees Description: <p>Longitude the specimens were collected, West is negative</p> http://lod.bco-dmo.org/id/dataset-parameter/985651.rdf Name: Date_specimen_collected Units: unitless Description: <p>Date the specimens were collected</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 7024 https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/0e634bf2-806f-40a4-8be1-61ef74e1ba59/content download https://doi.org/10.26008/1912/bco-dmo.985619.1 download onLine dataset &lt;p&gt;&lt;strong&gt;Collection&lt;/strong&gt;&lt;/p&gt; &lt;p&gt;Specimens of&amp;nbsp;&lt;em&gt;Diadema antillarum&lt;/em&gt; (urn:lsid:marinespecies.org:taxname:124332)&amp;nbsp; were collected by snorkel and transported to the lab in seawater buckets. The specimens were photographed, and vivisected into tissue components (body wall, spine, gonad, digestive tract and coelomic fluid), which were then frozen in liquid N2 for transport to the laboratory at Cornell University.&amp;nbsp;&lt;/p&gt; &lt;p&gt;&lt;strong&gt;Transcriptomic Sequencing&amp;nbsp;&lt;/strong&gt;&lt;/p&gt; &lt;p&gt;Transcriptomes from coelomic fluid of grossly normal (&lt;em&gt;n&lt;/em&gt;&amp;nbsp;=&amp;nbsp;2) and abnormal (&lt;em&gt;n&lt;/em&gt;&amp;nbsp;=&amp;nbsp;2) individuals from an affected site and of grossly normal individuals from a reference site (&lt;em&gt;n&lt;/em&gt;&amp;nbsp;=&amp;nbsp;2) were prepared alongside grossly normal (&lt;em&gt;n&lt;/em&gt;&amp;nbsp;=&amp;nbsp;2) aboral body wall tissues from a reference site to examine expressed genes and microorganisms associated with infection. RNA was extracted from coelomic fluid (300&amp;nbsp;μl) and body wall tissues (200 mg) using the Zymo Quick-RNA Tissue/Insect Kit using on-column deoxyribonuclease I digestion per the manufacturer’s protocols. Transcriptome libraries were prepared from purified RNA extracts using the Zymo RiboFree kit and sequenced on a single run of Illumina MiSeq using a Nextera DNA Library Prep Kit at the Biotechnology Resource Center at Cornell University. All sequences have been deposited at National Center for Biotechnology Information (NCBI) Sequence Read Archive under Bioproject&amp;nbsp;PRJNA900371 and SRA&amp;nbsp;accession numbers SRR22260770 to SRR22260777.&lt;/p&gt; &lt;p&gt;&lt;strong&gt;Viral Metagenomic Sequencing&lt;/strong&gt;&lt;/p&gt; &lt;p&gt;Small subsamples of each specimen were prepared for viral metagenomic sequencing broadly following the approach of Ng et al. (2011). Briefly, tissues were homogenized in sterile, 0.02&amp;nbsp;µm filtered phosphate buffered saline by beating using Zymo ZR Basher Beads (part number S6012-50) in a Biospec Instruments homogenizer for 1 min at maximum speed. The homogenates were centrifuged at 3,000 × g for 1 min to remove large cell debris, before filtering the supernatant through 0.2&amp;nbsp;µm pore size polyethersulfone syringe filters. Filtered homogenates were treated with 5U Turbo DNase (Invitrogen; part number AM2238), 5U Benzonase nuclease (Sigma Aldrich; part number E1014) and 20U RNase ONE (Promega; part number M4261) for 2 hours at 37&amp;nbsp;°C to digest extracellular and non-ribosome-bound nucleic acids. Following incubation, RNA was extracted from subsamples of purified virus-sized material using the Zymo Viral RNA kit (part number R1034) before storing RNA at −80&amp;nbsp;°C until further processing.&lt;/p&gt; &lt;p&gt;RNA in viral extracts was amplified using the SeqPlex RNA kit (Sigma Aldrich; part number SEQXE-10RXN, &lt;em&gt;n&lt;/em&gt;&amp;nbsp;=&amp;nbsp;11 libraries). Subsequent specimens were amplified using the TransPlex kit (WTA2; Sigma Aldrich; part number WTA2-10RXN, &lt;em&gt;n&lt;/em&gt;&amp;nbsp;=&amp;nbsp;3 libraries), which was used in prior RNA viral metagenomic work. Amplification products were purified using the Zymo DNA Clean and Concentrator -5 (part number D4004), quantified by Pico Green fluorescence (Invitrogen; part number P11496), and submitted for sequencing at the Cornell Biotechnology Resource Center. Libraries were prepared for sequencing using the Nextera Flex kit (Illumina; part number 20018704) and sequenced on the Illumina MiSeq platform using the 500 bp Nano kit. Sequences from all libraries were archived at NCBI under Bioproject PRJNA1117494 and SRA accessions SRR29258987 to SRR29258999.&lt;/p&gt; Specified by the Principal Investigator(s) - Imported &quot;Virome_Transcriptome_Metadata.txt&quot; into the BCO-DMO system - Converted &quot;Date&quot; to ISO 8601 YYYY-MM-DD format - Removed the N and W indicators, in accordance with BCO-DMO style for the &quot;Latitude&quot; and &quot;Longitude&quot;, making the W values negative - Renamed NCBI identifier fields to include more standard and descriptive titles - Exported file as &quot;985619_v1_virome_transcriptome.csv&quot; Scientific names in the data were checked using World Register of Marine Species (WoRMS) Taxon Match. All scientific names in the data are valid and accepted names as of 2025-10-01. 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 Illumina MiSeq Illumina MiSeq PI Supplied Instrument Name: Illumina MiSeq PI Supplied Instrument Description:Transcriptome libraries were prepared from purified RNA extracts using the Zymo RiboFree kit and sequenced on a single run of Illumina MiSeq using a Nextera DNA Library Prep Kit at the Biotechnology Resource Center at Cornell University. 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. Photographed Photographed PI Supplied Instrument Name: Photographed PI Supplied Instrument Description:The specimens were photographed, and vivisected into tissue components (body wall, spine, gonad, digestive tract and coelomic fluid), which were then frozen in liquid N2 for transport to the laboratory at Cornell University.  Instrument Name: Camera Instrument Short Name:camera Instrument Description: All types of photographic equipment including stills, video, film and digital systems. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/311/ Centrifuge Centrifuge PI Supplied Instrument Name: Centrifuge PI Supplied Instrument Description:The homogenates were centrifuged at 3,000 × g for 1 min to remove large cell debris, before filtering the supernatant through 0.2 µm pore size polyethersulfone syringe filters. Instrument Name: Centrifuge Instrument Short Name: Instrument Description: A machine with a rapidly rotating container that applies centrifugal force to its contents, typically to separate fluids of different densities (e.g., cream from milk) or liquids from solids. Snorkel Snorkel PI Supplied Instrument Name: Snorkel PI Supplied Instrument Description:Specimens were collected by snorkel and transported to the lab in seawater buckets.  Instrument Name: Diving Mask and Snorkel Instrument Short Name: Instrument Description: A diving mask (also half mask, dive mask or scuba mask) is an item of diving equipment that allows underwater divers, including, scuba divers, free-divers, and snorkelers to see clearly underwater. Snorkel: A breathing apparatus for swimmers and surface divers that allows swimming or continuous use of a face mask without lifting the head to breathe, consisting of a tube that curves out of the mouth and extends above the surface of the water. Biospec Instruments homogenizer Biospec Instruments homogenizer PI Supplied Instrument Name: Biospec Instruments homogenizer PI Supplied Instrument Description:Briefly, tissues were homogenized in sterile, 0.02 µm filtered phosphate buffered saline by beating using Zymo ZR Basher Beads (part number S6012-50) in a Biospec Instruments homogenizer for 1 min at maximum speed. Instrument Name: Homogenizer Instrument Short Name:Homogenizer Instrument Description: A homogenizer is a piece of laboratory equipment used for the homogenization of various types of material, such as tissue, plant, food, soil, and many others. Incubator Incubator PI Supplied Instrument Name: Incubator PI Supplied Instrument Description:Filtered homogenates were treated with 5U Turbo DNase (Invitrogen; part number AM2238), 5U Benzonase nuclease (Sigma Aldrich; part number E1014) and 20U RNase ONE (Promega; part number M4261) for 2 hours at 37 °C to digest extracellular and non-ribosome-bound nucleic acids. Following incubation, RNA was extracted from subsamples of purified virus-sized material using the Zymo Viral RNA kit (part number R1034) before storing RNA at −80 °C until further processing. Instrument Name: Incubator Instrument Short Name:incubator (general) Instrument Description: A device in which environmental conditions (light, photoperiod, temperature, humidity, etc.) can be controlled. Note: we have more specific terms for shipboard incubators (https://www.bco-dmo.org/instrument/629001) and in-situ incubators (https://www.bco-dmo.org/instrument/494).