1b:I[42426,["/_next/static/immutable/chunks/1xctgzqre-wsy.js","/_next/static/immutable/chunks/06_-wz6pdtp2b.js","/_next/static/immutable/chunks/30e52g49hg40p.js","/_next/static/immutable/chunks/02yq6tul2z-oh.js","/_next/static/immutable/chunks/10bx_ec2vj7n_.js","/_next/static/immutable/chunks/33bfn03fo8xnt.js","/_next/static/immutable/chunks/0tfjf78scu61b.js","/_next/static/immutable/chunks/31xnvej4n1bi9.js"],"default"] 1c:Td48,

Golf ball-sized coral fragments were collected by divers on SCUBA with hammers and chisels from two reefs in St. Thomas, United States Virgin Islands (USVI) showing signs of active SCTLD in February of 2020: Buck Island (18.27883˚, –64.89833˚) and Black Point (18.3445˚, –64.98595˚). Black Point, a nearshore reef, first exhibited SCTLD cases between December 2018 and January 2019, as documented in Brandt et al. (2021). Buck Island, situated near an offshore undeveloped island, recorded its first cases of SCTLD in October 2019, also documented in Brandt et al. (2021). Current environments at both sites are similar. SCTLD-affected corals were identified based on displaying acute multifocal lesions consistent with the SCTLD case definition at the time (SCTLD Case Definition, 2018). Lesions were bright white where the skeleton had recently been denuded of tissue, with no visible algal colonization at the skeletal/tissue boundary, indicating actively expanding lesions.

At both sites, one coral fragment was collected from each apparently healthy colony (Buck Island, n=3; Black Point, n=3), termed apparently healthy tissue on an apparently healthy colony (HH). Two fragments were collected from each diseased colony: one immediately adjacent to the SCTLD lesion line (Buck Island, n=3; Black Point, n=5), termed lesion tissue on a diseased colony (LD), and one as far away from the lesion line as possible (approximately 10 cm from the lesion line) (Buck Island, n=3; Black Point, n=5), termed apparently healthy tissue on a diseased colony (HD). The sampling scheme aimed to capture the variability in gene expression across different tissue health states while ensuring consistency in sampling methodology. Coral fragments were placed in individual bags that were sealed and transported to land on ice before being flash-frozen at -80˚C.

Total RNA was extracted from all 22 coral fragments following the protocol outlined in Beavers et al. (2023) using the RNAqueous-4PCR Total RNA Isolation Kit from Invitrogen (Life Technologies AM1914). About one gram of frozen coral tissue was scraped off each fragment into a 2 mL microcentrifuge tube using a sterilized bone cutter. Lysis buffer was added to each microcentrifuge tube followed by mechanical disruption using a refrigerated Qiagen Tissuelyser II at 30 oscillations/s for 60 s. Elution was performed in two 30 µL steps at a time. After combining elutions, contaminating DNA and chromatin were removed using the Ambion DNase I kit from Invitrogen (Life Technologies AM 2222). Resulting total RNA samples were sent to Novogene Co., LTD (Beijing, China) for quality assessment using an Agilent Bioanalyzer 2100. All 22 samples passed quality assessment with RNA integrity (RIN) values ≥ 7 and were preprocessed for mRNA enrichment using polyA tail capture. cDNA libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit from Illumina and sequenced on the Illumina NovaSeq 6000 for 150 bp, paired-end sequencing. Sample and data analysis was performed in January 2024.

The data have been deposited with links to BioProject accession number PRJNA1062758 in the NCBI BioProject database (https://www.ncbi.nlm.nih.gov/bioproject/).

1d:T6c0,These data include raw RNAseq reads from Montastraea cavernosa collected from two reefs in St. Thomas, United States Virgin Islands. Samples were collected from two reefs showing signs of active stony coral tissue loss disease (SCTLD) in February of 2020: Buck Island and Black Point. Black Point, a nearshore reef, first exhibited cases of SCTLD between December 2018 and January 2019, whereas Buck Island, situated near an offshore undeveloped island, recorded its first cases of SCTLD in October 2019. At both sites, one coral fragment was collected from each apparently health colony (Buck Island, n = 3; Black Point, n = 3), termed apparently healthy tissue on an apparently healthy colony (HH). Two fragments were collected from each diseased colony: one immediately adjacent to the SCTLD lesion line (Buck Island, n = 3: Black Point, n = 5), termed lesion tissue on a diseased colony (LD), and one as far away from the lesion line as possible (approximately 10 cm from the lesion line) (Buck Island, n = 3; Black Point, n = 5), termed apparently healthy tissue on a diseased colony (HD). Sample and data analysis was performed in January 2024. Sequences were used in a feature selection algorithm to identify the genes in M. cavernosa and its dominant algal endosymbiont, Cladocopium goreaui, that best discriminate between the three SCTLD health states. By characterizing the gene expression profiles associated with various tissue health states in M. cavernosa and C. goreaui, this data supports evidence that SCTLD causes dysbiosis between the coral host and its Symbiodiniaceae and describes the metabolic and immune shifts that occur as the holobiont transitions from an apparently healthy state to a diseased state.1e:Te2a,NSF Award Abstract: Coral reef ecosystems provide substantial economic resources to the societies of the United States Virgin Islands (USVI) and other US locations in the forms of tourism, fishing and coastal protection. However, reefs are among the most threatened marine environments, and coral disease is having a devastating impact on these valued systems. In early 2019, a multi-species rapid tissue loss disease matching the description of stony coral tissue loss disease (SCTLD) was found severely affecting a reef off the southwest coast of St. Thomas in the US Virgin Islands (USVI). SCTLD has been devastating coral reef communities in southeast Florida for the last four years, and was very recently reported from disparate areas around the Caribbean, including Mexico, Jamaica, and St. Martin. Rapid surveys by the investigators at the University of the Virgin Islands believe that a 50 km2 area southwest of St. Thomas is the initial incidence area of the disease, but will likely spread across the USVI, British Virgin Islands, and Puerto Rico. This study performs experiments to understand how this disease affects coral species immune traits and compares the microbiology and physiology of disease samples in the USVI to samples from Florida. It also examines how changing the species composition of a coral community affects the spread and impact of the disease. The overall aim is to produce a model to predict the impact of multi-species disease spread on reefs based on coral species assemblages. The project contributes to the research training of at least 2 undergraduates, 2 M.S. students, and 3 Ph.D. students, who benefit from cross-investigator mentoring. The research team includes representatives to the Coral Disease Advisory Committees for the USVI and Florida, which ensures rapid communication of findings to management bodies in both regions. Coral disease is a significant and increasing threat to Caribbean coral reef systems. Recent results demonstrate that coral species immune traits can predict disease resistance, and thus, forecast impacts to coral community structure, under multi-species coral disease. The onset of this epizootic in the USVI offers an unprecedented opportunity to test hypotheses about the impact of coral resistance, tolerance and immune traits on disease spread during the early stages of an outbreak that could profoundly change the diversity of Caribbean reefs. It is hypothesized that the abundance of highly susceptible species dictates 1) the onset of disease at reef sites downstream of the initial incidence area, and 2) the spread of disease within reef sites. Furthermore, 3) downstream reef sites where highly susceptible species are removed or treated show lower immune responses in all susceptible corals, later onset of disease, and slower within-site disease spread. To test these hypotheses, two experiments directly compare species responses to disease exposure and test the effect of species assemblage on coral immune function and disease spread. Results from these experiments aim to inform a generalizable model to predict the impact of multi-species disease spread on reefs based on coral species assemblages. Results of this project include direct comparison of the USVI disease to Florida SCTLD and a better understanding of how the abundance of highly susceptible host species impacts the spread of disease during the early onset of a multi-species panzootic. 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.6:["$","$L1b",null,{"dataset":{"_id":"935630","description":"","problem":"","acquisition":"$1c","processing":"

The data presented are raw RNAseq reads and have not undergone any processing besides that done at the sequencing facility.

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Removed the units from the columns named Reef_depth_m, Disease_Colony_Sample_Distance_cm, Temperature_C, and Salinity_psu.\r\n\r\nConverted the date format in the column Collection_month_year from Month name and two digit year to the ISO8601 format of YYYY-MM.\r\n\r\nRenamed the column Collection_month_year to Collection_Date.\r\n\r\nChecked the Coral Species name \"Montastraea cavernosa\" with the World Register of Marine Species (WoRMS) website to verify this is the accepted species name.\r\n\r\n\r\nSaved the dataset to the primary data file named 935630_v1_rna_seq_montastraea_cavernosa.\r\n\r\n\r\n\r\n","title":"RNAseq data from apparently healthy and Stony Coral Tissue Loss Disease-affected Montastraea cavernosa coral collected from St. Thomas, US Virgin Islands in 2020","nickname":"NCBI accessions for RNAseq data from apparently healthy and SCTLD-affected Montastraea cavernosa","dataUrl":"","currentState":"Final no updates expected","currentStateId":"7","validated":true,"restricted":false,"version":"1","version_date":"2024-12-10T05:00:00.000Z","abstract":"$1d","citation":"Beavers, K., Mydlarz, L. 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unique sample identification or number; any combination of alpha numeric characters; precise definition is file dependent

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NCBI BioProject accession number

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The National Center for Biotechnology Information (NCBI) BioProject identifier.

A BioProject is a collection of biological data related to a single initiative, originating from a single organization or from a consortium. A BioProject record provides users a single place to find links to the diverse data types generated for that project.

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NCBI BioSample accession number

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The National Center for Biotechnology Information (NCBI) BioSample accession number in the BioSample database.

The BioSample database stores descriptive information about the physical biological materials used to generate data submitted to NCBI's primary data archives. Typical examples of a BioSample include a cell line, a tissue biopsy or an environmental isolate. The BioSample database promotes the use of structured and consistent attribute names and values to describe sample properties and provenance. BioSample records are reciprocally linked to data derived from that sample and to the BioProjects in which they participate.

This identifier usually begins with SAMN

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NCBI SRA accession number

","units":{"_id":"","name":"unitless"},"type":{"_id":"856992","name":"SRA_run","description":"

The National Center for Biotechnology Information (NCBI) Run accession in the Sequence Read Archive (SRA).

Results are called runs in the SRA. Runs comprise the data gathered for a sample or sample bundle and refer to a defining experiment.

A Run is an object that contains actual sequencing data for a particular sequencing experiment. Experiments may contain many Runs depending on the number of sequencing instrument runs that were needed.

This identifier usually begins with SRR

"}},{"_id":"945742","name":"Sample_type","format":"","frictionlessType":"string","description":"

Type of sample collected. Tissue fragment = a golf ball-sized fragment of coral tissue + skeleton that we later extracted RNA from

","units":{"_id":"","name":"unitless"},"type":{"_id":"1742","name":"sample_type","description":"

text description of type of sample collected (rock, bio, fluid, etc)

"}},{"_id":"945743","name":"Coral_species","format":"","frictionlessType":"string","description":"

Species of Coral collected: All samples were collected from Montastraea cavernosa colonies

","units":{"_id":"","name":"unitless"},"type":{"_id":"976","name":"species","description":"

a taxonomic binomial that consists of a genus name followed by the species name of an organism

"}},{"_id":"945744","name":"Reef_Name","format":"","frictionlessType":"string","description":"

The name of the reef that samples were collected from

","units":{"_id":"","name":"unitless"},"type":{"_id":"952","name":"region","description":"

geographical area of sampling

"}},{"_id":"945745","name":"Reef_type","format":"","frictionlessType":"string","description":"

Indicates the reef type that samples were collected from

","units":{"_id":"","name":"unitless"},"type":{"_id":"1740","name":"site_descrip","description":"

Description or characteristics of a sampling site

"}},{"_id":"945746","name":"Collection_Date","format":"%Y-%m","frictionlessType":"date","description":"

Indicates the month and year of sample collection

","units":{"_id":"","name":"unitless"},"type":{"_id":"1070","name":"date","description":"

date; generally reported in GMT as YYYYMMDD (year; month; day); also as MMDD (month; day); EqPac dates are local Hawaii time. ISO_Date format is YYYY-MM-DD (http://www.iso.org/iso/home/standards/iso8601.htm)

"}},{"_id":"945747","name":"Latitude","format":"","frictionlessType":"number","description":"

Sampling location latitude, south is negative

","units":{"_id":"","name":"decimal degrees"},"type":{"_id":"730","name":"latitude","description":"

latitude, in decimal degrees, North is positive, negative denotes South; Reported in some datasets as degrees, minutes

"}},{"_id":"945748","name":"Longitude","format":"","frictionlessType":"number","description":"

Sampling location longitude, west is negative

","units":{"_id":"","name":"decimal degrees"},"type":{"_id":"731","name":"longitude","description":"

longitude, in decimal degrees, East is positive, negative denotes West; Reported in some datasets as degrees, minutes

"}},{"_id":"945749","name":"SCTLD_duration_months","format":"","frictionlessType":"integer","description":"

Indicates in months how long SCTLD had been present at that location prior to sampling

","units":{"_id":"","name":"unitless"},"type":{"_id":"555754","name":"duration","description":"

Duration of treatment, observation or sampling

"}},{"_id":"945750","name":"Reef_depth","format":"","frictionlessType":"number","description":"

The depth of the sample collected

","units":{"_id":"","name":"meters (m)"},"type":{"_id":"808","name":"depth","description":"

Observation/sample depth below the sea surface. Units often reported as: meters, feet.

\nWhen used in a JGOFS/GLOBEC dataset the depth is a best estimate; usually but not always calculated from pressure; calculated either from CTD pressure using Fofonoff and Millard (1982; UNESCO Tech Paper #44) algorithm adjusted for 1980 equation of state for seawater (EOS80) or simply equivalent to nominal depth as recorded during sampling if CTD pressure was unavailable.

"}},{"_id":"945751","name":"Temperature","format":"","frictionlessType":"number","description":"

The temperature of sample environment

","units":{"_id":"","name":"Celcius (degC)"},"type":{"_id":"733","name":"temperature","description":"

water temperature at measurement depth

"}},{"_id":"945752","name":"Salinity","format":"","frictionlessType":"number","description":"

The salinity of the sample environment

","units":{"_id":"","name":"psu"},"type":{"_id":"955","name":"sal","description":"

Salinity: The amount (mass or quantity of matter) of salt per amount (volume or mass) of a body of water.

"}},{"_id":"945753","name":"pH","format":"","frictionlessType":"number","description":"

The pH of the sample environment

","units":{"_id":"","name":"unitless"},"type":{"_id":"1892","name":"pH","description":"

pH: The measure of the acidity or basicity of an aqueous solution

"}},{"_id":"945754","name":"Colony_status","format":"","frictionlessType":"string","description":"

The health status of the colony sampled. (Diseased = SCTLD; Healthy = Apparently healthy)

","units":{"_id":"","name":"unitless"},"type":{"_id":"990","name":"status","description":"

state of the data, (e.g. new, pending, collected, raw)

"}},{"_id":"945755","name":"Frag_condition","format":"","frictionlessType":"string","description":"

The tissue status of the sample (Apparently healthy = apparently healthy (visibly); Lesion = immediately adjacent to the SCTLD lesion)

","units":{"_id":"","name":"unitless"},"type":{"_id":"990","name":"status","description":"

state of the data, (e.g. new, pending, collected, raw)

"}},{"_id":"945756","name":"Tissue_Health_State","format":"","frictionlessType":"string","description":"

The health state identifier of the sample (HH = apparently healthy tissue from an apparently healthy colony; HD = apparently healthy tissue from a SCTLD-affected colony; LD = lesion tissue from a SCTLD-affected colony)

","units":{"_id":"","name":"unitless"},"type":{"_id":"990","name":"status","description":"

state of the data, (e.g. new, pending, collected, raw)

"}},{"_id":"945757","name":"Disease_Colony_Sample_Distance","format":"","frictionlessType":"integer","description":"

Indicates how far away the apparently healthy tissue was sampled from the SCTLD lesion (only applies to HD tissue). nd = not collected (HH or LD)

","units":{"_id":"","name":"centimeters (cm)"},"type":{"_id":"1073","name":"no_bcodmo_term","description":"

An association with a community-wide standard parameter has not yet been made.

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RNA-Seq = samples were prepared for RNA sequencing

","units":{"_id":"","name":"unitless"},"type":{"_id":"927354","name":"sequencing description","description":"

Term describing the methodology and description of sequencing (often used for NCBI run descriptions: library selection, strategy, source, ...).

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all RNA samples were prepared for 150 base-pair, paired-end sequencing

","units":{"_id":"","name":"unitless"},"type":{"_id":"927354","name":"sequencing description","description":"

Term describing the methodology and description of sequencing (often used for NCBI run descriptions: library selection, strategy, source, ...).

"}},{"_id":"945760","name":"Sequencing_Instrument_model","format":"","frictionlessType":"string","description":"

All RNA samples were sequenced on the Illumina NovaSeq 6000

","units":{"_id":"","name":"unitless"},"type":{"_id":"1758","name":"inst_model","description":"

Instrument Model

"}},{"_id":"945761","name":"Sequencing_strategy_details","format":"","frictionlessType":"string","description":"

All RNA samples were processed for polyA-tail enrichment to remove non-eukaryotic reads

","units":{"_id":"","name":"unitless"},"type":{"_id":"927354","name":"sequencing description","description":"

Term describing the methodology and description of sequencing (often used for NCBI run descriptions: library selection, strategy, source, ...).

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Indicates how the RNA was extracted from each sample.

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Term describing the methodology and description of sequencing (often used for NCBI run descriptions: library selection, strategy, source, ...).

"}}],"related_publications":[{"id":"946346","citation":"Beavers, K. M., Gutierrez-Andrade, D., Van Buren, E. W., Emery, M. A., Brandt, M. E., Apprill, A., & Mydlarz, L. D. (2024). Characterizing gene expression profiles of various tissue states in stony coral tissue loss disease using a feature selection algorithm. https://doi.org/10.1101/2024.11.05.622084\r\n","relation_type":["Results"],"relation_desc":""},{"id":"945722","citation":"Beavers, K. M., Van Buren, E. W., Rossin, A. M., Emery, M. A., Veglia, A. J., Karrick, C. E., MacKnight, N. J., Dimos, B. A., Meiling, S. S., Smith, T. B., Apprill, A., Muller, E. M., Holstein, D. M., Correa, A. M. S., Brandt, M. E., & Mydlarz, L. D. (2023). Stony coral tissue loss disease induces transcriptional signatures of in situ degradation of dysfunctional Symbiodiniaceae. Nature Communications, 14(1). https://doi.org/10.1038/s41467-023-38612-4\r\n","relation_type":["Methods"],"relation_desc":""},{"id":"945721","citation":"Brandt, M. E., Ennis, R. S., Meiling, S. S., Townsend, J., Cobleigh, K., Glahn, A., Quetel, J., Brandtneris, V., Henderson, L. M., & Smith, T. B. (2021). The Emergence and Initial Impact of Stony Coral Tissue Loss Disease (SCTLD) in the United States Virgin Islands. Frontiers in Marine Science, 8. https://doi.org/10.3389/fmars.2021.715329\r\n","relation_type":["Methods"],"relation_desc":""},{"id":"945723","citation":"SCTLD Case Definition. (2018). Florida Coral Disease Response Research & Epidemiology Team. https://floridadep.gov/sites/default/files/Copy%20of%20StonyCoralTissueLossDisease_CaseDefinition%20final%2010022018.pdf\r\n","relation_type":["Methods"],"relation_desc":""}],"related_datasets":[{"_id":"833133","name":"SCTLD rapid microbiome characterization","url":"","relation_type":"IsRelatedTo","type_desc":"

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\n","relation_desc":"","citation":"Apprill, A., Brandt, M. (2021) Application of a rapid microbiome characterization pipeline to corals afflicted with Stony Coral Tissue Loss Disease in St. Thomas, US Virgin Islands. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2020-12-07 doi:10.26008/1912/bco-dmo.833133.1"},{"_id":"","name":"","url":"https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1062758","relation_type":"IsRelatedTo","type_desc":"The dataset is related to another dataset.","relation_desc":"","citation":"University of Texas at Arlington (2025). RNASeq data from multiple SCTLD health states of Montastraea cavernosa from a natural reef environment in the US Virgin\r\nIslands. 2025/01. NCBI:BioProject: PRJNA1062758 [Internet]. Bethesda, MD: National Library of Medicine (US), National Center for Biotechnology Information; Available from: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1062758. "}],"services":[{"grouping":"","items":[{"name":"View Data","description":"An in-browser view of the primary tabular data file","url":"https://www.bco-dmo.org/dataset/935630/data/view","contentType":"text/html","actionType":"view"}]},{"grouping":"Metadata","items":[{"name":"HTML","description":"A simple HTML page of the dataset metadata","url":"https://www.bco-dmo.org/dataset/935630/description","contentType":"text/html","actionType":"view"},{"name":"PDF","description":"A PDF of the HTML dataset metadata","url":"https://www.bco-dmo.org/dataset/935630/Dataset_description.pdf","contentType":"application/pdf","actionType":"download"},{"name":"ISO 19115-2 (NOAA Profile)","description":"","url":"https://www.bco-dmo.org/dataset/935630/iso","contentType":"application/xml","actionType":"download"}]}],"programs":[],"projects":[{"_id":"811115","name":"RAPID: Collaborative Research: Predicting the Spread of Multi-Species Coral Disease Using Species Immune Traits","acronym":"Multi-Species Coral Disease","description":"$1e"}],"archives":[{"id_value":"10.26008/1912/bco-dmo.935630.1","url":"https://doi.org/10.26008/1912/bco-dmo.935630.1","date_assigned":"2024-12-19","version_date":"2024-12-10","archiver":"Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)","archiver_id":"272"}],"license":{"name":"Creative Commons Attribution 4.0","id":"CC-BY-4.0","uri":"https://creativecommons.org/licenses/by/4.0/","spdxUri":"https://spdx.org/licenses/CC-BY-4.0"},"metrics":{"views":{"count":211},"downloads":{"count":263}}},"fileId":"946366"}]