14:I[71133,["4507","static/chunks/e2799680-446c489506865058.js","7665","static/chunks/7665-81c5407bc4489ff9.js","8500","static/chunks/8500-e4dd1cb1bb626827.js","9753","static/chunks/9753-028c0a26aa71f2d4.js","8437","static/chunks/8437-a09d0b83fcec76af.js","4557","static/chunks/4557-64c5efa221bc528f.js","947","static/chunks/947-410627998426400f.js","5357","static/chunks/5357-6142894e88cb7da2.js","8382","static/chunks/app/dataset/%5Bid%5D/data/view/page-177ea8adea7aed86.js"],"default"] 15:T1c44,

Sample Collection:
Following the disease outbreak, fifteen samples of Pseudodiploria strigosa corals were collected in the Flower Garden Banks National Marine Sanctuary at the West Flower Garden Bank (Buoy 2: 27.875433, -93.813933 and Buoy 5: 27.875317, -93.814817) and East Flower Garden Bank (Buoy 2: 27.9086, -93.597183). Samples were collected on SCUBA using a hammer and chisel at a depth range of 61 to 70 feet. Corals (n = 10 colonies) were sampled in situ as sets of diseased and apparently healthy P. strigosa, where two samples were collected per diseased coral (DD: adjacent to the tissue loss lesion, n = 5; HD: apparently healthy tissue on the same coral, n = 5) and one sample was collected from a neighboring apparently healthy conspecific coral (HH; n = 5). Each sample was divided into three fragments that were preserved for histopathology (data not included herein), transmission electron microscopy (TEM), and DNA/RNA sequencing. Histopathology tissue samples were fixed in zinc-buffered formalin (Z-fix concentrate from Anatech Ltd. diluted with filtered seawater) for 24 hours, washed with seawater for 24 hours, then stored in 70% ethanol for transport to Louisiana State University, Baton Rouge, LA, USA. TEM samples were preserved in 750 microliters (µL) of 2% PFA in 3X PBS at 4 degrees Celsius (ºC) for transport to Rice University, Houston, TX, USA. For DNA/RNA extraction, samples were collected, flash frozen in liquid nitrogen, and stored at -150ºC for transport to the University of Texas at Arlington, Arlington, TX, USA.

Transmission Electron Microscopy (TEM) Imaging:
Coral fragments ~3 square millimeters (mm²) in size (fixed in 750 µL of 2% PFA in 3X PBS) were decalcified in 1000 µL of 1.5% ascorbic acid for 7-14 days, replacing the ascorbic acid solution daily until the entire skeleton was dissolved. The decalcified samples were fixed in Karnovsky's fixative for at least 24 hours before being post-fixed and processed according to (Howe-Kerr et al., 2023). Electron micrographs were imaged using a 120 kV JEOL JEM-1400Flash Transmission Electron Microscope equipped with a high-contrast pole piece and a 15 megapixel AMT NanoSprint15 sCMOS camera. Electron micrographs showed 438 total Symbiodiniaceae cells: 123 from HH tissue (20-30 cells per sample), 142 from HD tissue (23-38 cells per sample), and 173 from DD tissue (27-46 cells per sample). Electron micrographs were labelled by cell ID and grouped into separate pdf files per sample.

Nucleic Acid Extraction and Sequencing:
Subsets of the fifteen P. strigosa samples were first extracted for total RNA using a pea-sized amount of coral tissue harvested from the frozen samples using stainless steel sterilized bone cutters. For DD samples, the tissue was taken ~1 to 2 centimeters from the visible lesion line. Extractions were conducted using the Invitrogen RNAqueous Kit (AM1914). Potential DNA and chromatin contamination was removed from each sample using the Ambion DNase I (RNase-free) kit from Invitrogen (Life Technologies AM2222). Total RNA aliquots were sent to Novogene Co., LTD for library preparation and paired-end sequencing. All 15 P. strigosa samples had an RNA integrity number (RIN) ≥ 4 and were pre-processed with poly-A tail enrichment to capture all eukaryotic reads. Library prep was completed using the NEBNext Ultra II RNA Library Prep kit by Illumina and samples were processed for 150bp, paired-end sequencing on the Illumina Novaseq 6000 platform with raw read file sizes at a minimum of 5 million.

Upon confirmation of successful RNA extraction, DNA was extracted from the remainder of each coral. Coral samples were airbrushed with a PBS solution to remove coral tissue from the skeleton. The resulting tissue slurry was spun in a centrifuge at maximum speed at 4ºC for 40 minutes or until there was a well-formed pellet with near-transparent supernatant. DNA was extracted from ~0.040 grams (g) of the pelleted coral holobiont biomass with the Qiagen DNeasy PowerBioFilm Kit (Qiagen, Inc., Germantown, MD, 24000-50) according to the manufacturer's protocol and stored at -80ºC until further processing. One 50 µL aliquot of extracted DNA was transferred to Rice University and another was transferred to Woods Hole Oceanographic Institution for sequencing of Symbiodiniaceae ITS-2 rDNA and 16S rRNA genes for bacteria/archaea, respectively.

To characterize Symbiodiniaceae composition, the ITS-2 region of Symbiodiniaceae rDNA was PCR amplified with the Sym_VAR primer set (Sym_VAR_5.8SII and Sym_VAR_REV; Hume et al., 2018). Each 16 µL PCR reaction contained: 1 µL DNA template, 9 µL EconoTaq PLUS GREEN 2X Master Mix (Biosearch Technologies), 0.42 µL each of forward and reverse primer at 100 µM, and 5.16 µL DNAse/RNAse-free water. PCR reactions were cycled as: initial denaturation at 94°C for 3 minutes; followed by 35 cycles of 94°C for 75 seconds, 58°C for 75 seconds, and 74°C for 90 seconds; and a final extension at 74°C for 7 minutes, before holding at 4°C. Library preparation and ITS-2 sequencing were performed at Oregon State University's Center for Quantitative Life Sciences (OSU CQLS, Corvallis, OR, USA) with 2x300 bp paired-end reads on an Illumina MiSeq platform. Blanks (nuclease-free PCR-grade water) were used as negative controls during sequencing.

To characterize bacteria and archaea, single barcoded PCR reactions were performed to amplify the V4 region of the small subunit rRNA gene using primers 515FY and 806RB (Apprill et al., 2015; Parada et al., 2015). As a sequencing control, we used genomic DNA from Microbial Mock Community B (even, low concentration), v5.1L, HM-782D, and nuclease-free PCR-grade water for the negative control. Each 50 μL PCR reaction contained: 2 μL DNA template, 0.5 μL GoTaq DNA Polymerase (Promega), 1 μL of each forward and reverse primer at 10 micromolar (μM), 1 μL of 10 millimolar (mM) deoxynucleoside triphosphate (dNTP) mix (Promega), 5 μL MgCl₂, 10 μL GoTaq 5X colourless flexi buffer (Promega), and 29.5 μL nuclease-free water. The PCR cycling conditions were as follows: initial denaturation at 95°C for 2 minutes; followed by 34 or 37 cycles of 95°C for 20 seconds, 55°C for 15 seconds, and 72°C for 5 minutes; and a final extension at 72°C for 10 minutes, before holding at 4°C. We used 34 or 37 cycles for samples to obtain comparable amounts of amplified DNA for subsequent purification and sequencing. Barcoded PCR products were purified using the MinElute PCR Purification Kit (Qiagen, Inc., Germantown, MD), and concentrations were measured using a Qubit 2.0 fluorometer. Purified samples were diluted to 1 nanogram per microliter (ng/μL) and pooled for sequencing. Sequencing was performed with 2x250 bp paired-end reads on an Illumina MiSeq platform at the University of Illinois at Urbana-Champaign (Kozich et al., 2013). During analysis of the resulting fastq files, two samples (HD and DD tissues from coral 007) were excluded from analysis due to a mislabeling error during laboratory processing.

16:T487,This dataset includes microscopy and omics data associated with 15 apparently healthy and diseased Pseudodiploria strigosa corals collected from the Flower Garden Banks National Marine Sanctuary (Northwest Gulf of Mexico) in September 2022, one month after a coral disease outbreak. Samples were collected from pairs of apparently healthy corals (HH tissue; n=5) and diseased corals (n=5). From diseased corals, two tissue samples were taken: apparently healthy tissue (HD) and disease-adjacent tissue (DD). Histopathology light microscopy images and electron micrographs of Symbiodiniaceae cells generated with transmission electron microscopy (TEM) are included as PDF files sorted by sample. These data also include NCBI Sequence Read Archive (SRA) accession numbers for raw fastq files of 16S rRNA gene sequencing, internal transcribed spacer-2 (ITS-2) sequencing, and RNA-Seq. This dataset supports an integrative approach for characterizing signatures of marine diseases at cellular, sub-cellular, and gene expression levels spanning multiple holobiont members: the coral host, Symbiodiniaceae microeukaryotes, bacteria/archaea communities, and viruses.17:Tcb1,NSF Award Abstract: Marine diseases have devastating impacts on ocean ecosystems and this work directly informs understanding of disease transmission in the ocean. To understand the cause and patterns of spread of a disease outbreak that began in late summer of 2022 at the Flower Garden Banks National Marine Sanctuary (northwest Gulf of Mexico, GoM), a team of ecologists, ocean connectivity and disease modelers, microbiologists, and coral immunologists (from Rice University, the University of Virgin Islands (UVI), Louisiana State University (LSU), and Woods Hole Oceanographic Institution) is monitoring the health of corals, and biopsy their tissues. This data aid in developing a model that predicts coral disease transmission and its impacts on economically valuable coral reefs in the GoM. This project supports multidisciplinary field and laboratory research experiences of graduate students at multiple minority-serving institutions, and provides 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 collaboratively provides URM students with research experiences in STEM fields. Project findings are being broadly communicated through virtual public programming, to the Disease Advisory Council, and via direct updates to managers of the Flower Garden Bank National Marine Sanctuary. Over the last four decades, diseases decimated ecosystem engineers in marine coastal environments, including coral reefs. Recent results from studies of white plague and stony coral tissue loss disease (SCTLD) show coral species immune traits can influence disease resistance and therefore predict of coral community structure post-outbreak in the Caribbean. In late August of 2022, an unidentified multi-species acute tissue loss disease with signs and species susceptibility characteristics reminiscent of white plague or SCTLD was documented at the Flower Garden Banks (northwest Gulf of Mexico, GoM). This disease is having significant impacts on FGB and could become widespread across the GoM, offering an opportunity to test hypotheses about the influence of coral community composition and pathogen dispersal on disease spread during the early stages of an outbreak; few studies examine this on relatively isolated, deep, coral-dense reefs. The interdisciplinary research team employs photomosaics and colony fate-tracking, layered molecular datasets and microscopy approaches, as well as modeling of disease reservoirs and dispersal to assess the etiology of the disease and contribute to the development of a generalizable framework for disease spread on reefs. By parsing the impacts of reef-scale community composition versus seascape-scale dispersal in disease transmission and persistence, this work helps reveal the potential resistance and resilience of isolated, coral-dense reefs to diseases that decimate these ecosystems across the wider Caribbean. 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:["$","$L14",null,{"dataset":{"_id":"1010240","description":"","problem":"Two samples (007_HD and 007_DD) do not have associated 16S data due to labeling errors during sample processing. One sample (004_HH) does not have an associated histology image due to data loss post-analysis.","acquisition":"$15","processing":"

Histology images and electron micrographs were sorted into separate pdf files per sample. Electron micrographs were labelled with a cell ID (starting with 1 per sample). Raw ITS-2, 16S, and RNA-seq sequences were uploaded to the NCBI Sequence Read Archive (SRA).

\n","bcodmoProcessing":"This section documents curation actions performed prior to publication review with the submitter, and additional information relevant to understanding and reusing this dataset. It distinguishes changes made to the submitted (meta)data from unresolved issues and/or enhancements that improve future reuse and interoperability.\r\n\r\nCURATION ACTIONS PERFORMED ON DATA\r\n\r\n- Imported original file \"FGB22_BCO-DMO_metadata_SRA.xlsx\" (sheet 1) into the BCO-DMO data processing system.\r\n- Treated \"NA\" as a missing value (Note: missing values are empty/blank in the final CSV file).\r\n- Converted collection_date from format %d-%b-%y to format %Y-%m-%d.\r\n- Saved the final file as \"1010240_v1_fgb22_pstr_coral_disease.csv\".\r\n\r\nCURATION ACTIONS PERFORMED ON METADATA\r\n\r\n- BCO-DMO's standard metadata entry and text formatting steps were performed. See: https://www.bco-dmo.org/how-to/standard-curation-edits\r\n\r\nISSUES POTENTIALLY IMPACTING REUSE\r\n\r\n- N/A","title":"Light microscopy images, Symbiodiniaceae electron micrographs, and NCBI Sequence Read Archive (SRA) accession numbers associated with diseased and healthy Pseudodiploria strigosa corals collected from the Flower Garden Banks National Marine Sanctuary","nickname":"FGB22 PSTR Coral Disease Microscopy & Omics","dataUrl":"","currentState":"Final","currentStateId":"7","validated":true,"restricted":false,"version":"1","version_date":"2026-10-20T04:00:00.000Z","abstract":"$16","citation":"Karrick, C. E., Swain, H. L., Rossin, A., Kastner, M., Apprill, A., Brandt, M., Holstein, D., Mydlarz, L., Correa, A. M. (2026) Light microscopy images, Symbiodiniaceae electron micrographs, and NCBI Sequence Read Archive (SRA) accession numbers associated with diseased and healthy Pseudodiploria strigosa corals collected from the Flower Garden Banks National Marine Sanctuary. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2026-10-20 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.1010240.1 [access date]","citationParts":{"identifier":"doi:10.26008/1912/bco-dmo.1010240.1","versionDate":"2026-10-20","versionId":"1","year":"2026","title":"Light microscopy images, Symbiodiniaceae electron micrographs, and NCBI Sequence Read Archive (SRA) accession numbers associated with diseased and healthy Pseudodiploria strigosa corals collected from the Flower Garden Banks National Marine Sanctuary","authors":"Karrick, C. E., Swain, H. L., Rossin, A., Kastner, M., Apprill, A., Brandt, M., Holstein, D., Mydlarz, L., Correa, A. M.","publisher":"Biological and Chemical Oceanography Data Management Office (BCO-DMO)."},"doi":"10.26008/1912/bco-dmo.1010240.1","release_date":null,"field_dataset_location":"Flower Garden Banks National Marine Sanctuary","temporal_extent":{"start":"2022-09-20T04:00:00.000Z","end":"2022-09-21T04:00:00.000Z"},"temporal":{"resolution":"time:unitDay","type":"time:Interval","start":{"value":"1663646400","label":"2022-09-20"},"end":{"value":"1663732800","label":"2022-09-21"}},"spatial_extent":{"shape":"polygon","center":{"latitude":27.891958499332,"longitude":-93.705999997761},"wkt":"POLYGON ((-93.814817 27.875317, -93.597183 27.875317, -93.597183 27.9086, -93.814817 27.9086, -93.814817 27.875317))","north":27.9086,"east":-93.597183,"south":27.875317,"west":-93.814817},"dataset_type":["Other Field Results"],"keywords":["oceans"],"data_files":[{"id":"1010463","title":"1010240_v1_fgb22_pstr_coral_disease.csv","url":"https://datadocs.bco-dmo.org/dataset/1010240/file/QAo5416f6JAP3v/1010240_v1_fgb22_pstr_coral_disease.csv","showTableUrl":"https://www.bco-dmo.org/dataset/1010240/data/view/1010463","description":"Primary data file for dataset ID 1010240, version 1","filename":"1010240_v1_fgb22_pstr_coral_disease.csv","bytesize":3086,"checksum":{"value":"e49ebab80a8b0bd0387e9110319b3cf2","Algorithm":{"_id":"190","name":"MD5"}},"mimetype":"text/csv","fileType":{"_id":"192","name":"Comma Separated Values (.csv)"},"isErddap":"bcodmo_dataset_1010240_v1","date":"","isPublicDuringEmbargo":false,"primaryDataFile":true,"showTable":true,"restricted":false}],"supplemental_files":[{"id":"1010462","title":"Microscopy images","url":"https://datadocs.bco-dmo.org/dataset/1010240/file/7DEW46psynMNL/FGB22_PSTR_microscopy.tar.gz","showTableUrl":"","description":"Supplemental file for dataset ID 1010240, version 1. Compressed folder containing all histopathology (i.e., light microscopy) images and Symbiodiniaceae electron micrographs.","filename":"FGB22_PSTR_microscopy.tar.gz","bytesize":1570686135,"checksum":{"value":"98f65b0d0d3edc22fee605a2a4beeb10","Algorithm":{"_id":"190","name":"MD5"}},"mimetype":"application/gzip","fileType":{"_id":"573","name":"GZIP (.gz)"},"isErddap":"","date":"","isPublicDuringEmbargo":false,"primaryDataFile":false,"showTable":false,"restricted":false}],"roles":[{"role":{"_id":"140","name":"Co-Principal Investigator"},"performedBy":{"_id":"553489","name":"Amy Apprill"},"performedAtOrganization":{"_id":"2","name":"Woods Hole Oceanographic Institution"}},{"role":{"_id":"140","name":"Co-Principal Investigator"},"performedBy":{"_id":"559376","name":"Marilyn Brandt"},"performedAtOrganization":{"_id":"514247","name":"University of the Virgin Islands Center for Marine and Environmental Studies"}},{"role":{"_id":"140","name":"Co-Principal Investigator"},"performedBy":{"_id":"713331","name":"Adrienne M.S. Correa"},"performedAtOrganization":{"_id":"151","name":"Rice University"}},{"role":{"_id":"140","name":"Co-Principal Investigator"},"performedBy":{"_id":"811122","name":"Daniel Holstein"},"performedAtOrganization":{"_id":"670530","name":"Louisiana State University"}},{"role":{"_id":"140","name":"Co-Principal Investigator"},"performedBy":{"_id":"51558","name":"Laura Mydlarz"},"performedAtOrganization":{"_id":"299","name":"University of Texas at Arlington"}},{"role":{"_id":"128","name":"Student"},"performedBy":{"_id":"997775","name":"Carly E. Karrick"},"performedAtOrganization":{"_id":"151","name":"Rice University"}},{"role":{"_id":"128","name":"Student"},"performedBy":{"_id":"988676","name":"Mallory Kastner"},"performedAtOrganization":{"_id":"2","name":"Woods Hole Oceanographic Institution"}},{"role":{"_id":"128","name":"Student"},"performedBy":{"_id":"1010280","name":"Ashley Rossin"},"performedAtOrganization":{"_id":"670530","name":"Louisiana State University"}},{"role":{"_id":"128","name":"Student"},"performedBy":{"_id":"1010277","name":"Hannah L. Swain"},"performedAtOrganization":{"_id":"299","name":"University of Texas at Arlington"}},{"role":{"_id":"145","name":"BCO-DMO Data Manager"},"performedBy":{"_id":"51498","name":"Shannon Rauch"},"performedAtOrganization":{"_id":"191","name":"Woods Hole Oceanographic Institution"}}],"deployments":[{"_id":"1010380","name":"FGB22","synonyms":["Coral Disease response cruise 2"],"dates":{"start":"2022-09-20T00:00:00.000Z","end":"2022-09-21T00:00:00.000Z"},"platform":{"_id":"787670","name":"R/V Manta"},"chiefScientists":[]}],"funding":[{"_id":"877262","name":"OCE-2109622","fundingSource":{"_id":"355","name":"NSF Division of Ocean Sciences"},"url":"https://www.nsf.gov/awardsearch/show-award?AWD_ID=2109622"},{"_id":"1002090","name":"OCE-2530272","fundingSource":{"_id":"355","name":"NSF Division of Ocean Sciences"},"url":"https://www.nsf.gov/awardsearch/show-award?AWD_ID=2530272"}],"instruments":[{"_id":"1010340","name":"Airbrush","description":"Airbrush: An airbrush was used to create coral tissue slurry for DNA extraction.","type_id":"657881","type_name":"Airbrush","type_desc":" Device for spraying liquid by means of compressed air.","type_acronym":"Airbrush"},{"_id":"1010333","name":"Illumina MiSeq","description":"Illumina MiSeq: 16S and ITS-2 sequencing was performed on an Illumina MiSeq platform (PE250 and PE300, respectively).","type_id":"649","type_name":"Automated DNA Sequencer","type_desc":"A DNA sequencer is an instrument that determines the order of deoxynucleotides in deoxyribonucleic acid sequences.","type_acronym":"Automated Sequencer"},{"_id":"1010334","name":"Illumina Novaseq 6000","description":"Illumina Novaseq 6000: RNA-seq was performed on an Illumina Novaseq 6000 platform.","type_id":"649","type_name":"Automated DNA Sequencer","type_desc":"A DNA sequencer is an instrument that determines the order of deoxynucleotides in deoxyribonucleic acid sequences.","type_acronym":"Automated Sequencer"},{"_id":"1010339","name":"Bone cutters","description":"Bone cutters: Sterile bone cutters were used to scrape coral tissue for RNA extraction.","type_id":"867860","type_name":"bone cutter","type_desc":"A bone cutter is a surgical instrument used to cut bones or coral fragments. ","type_acronym":""},{"_id":"1010341","name":"Centrifuge","description":"Centrifuge: A 4°C centrifuge was used to create a pellet of coral tissue slurry.","type_id":"629890","type_name":"Centrifuge","type_desc":"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.","type_acronym":""},{"_id":"1010342","name":"MinElute PCR Purification Kit","description":"MinElute PCR Purification Kit (Qiagen, Inc., Germantown, MD): Barcoded 16S PCR products were purified with the MinElute PCR Purification Kit (Qiagen, Inc., Germantown, MD).","type_id":"1000452","type_name":"DNA Analysis Kit","type_desc":"A laboratory kit containing reagents and materials used to extract, purify, detect, measure, or otherwise evaluate genetic material from a sample.","type_acronym":""},{"_id":"1010335","name":"Invitrogen RNAqueous Kit (AM1914)","description":"Invitrogen RNAqueous Kit (AM1914): RNA was extracted with the Invitrogen RNAqueous Kit (AM1914).","type_id":"1000452","type_name":"DNA Analysis Kit","type_desc":"A laboratory kit containing reagents and materials used to extract, purify, detect, measure, or otherwise evaluate genetic material from a sample.","type_acronym":""},{"_id":"1010336","name":"Ambion DNase I (RNase-free) kit from Invitrogen (Life Technologies AM2222)","description":"Potential DNA and chromatin contamination was removed from each sample using the Ambion DNase I (RNase-free) kit from Invitrogen (Life Technologies AM2222).","type_id":"1000452","type_name":"DNA Analysis Kit","type_desc":"A laboratory kit containing reagents and materials used to extract, purify, detect, measure, or otherwise evaluate genetic material from a sample.","type_acronym":""},{"_id":"1010337","name":"NEBNext Ultra II RNA Library Prep kit by Illumina","description":"NEBNext Ultra II RNA Library Prep kit by Illumina: Library preparation for RNA sequencing was completed with the NEBNext Ultra II RNA Library Prep kit by Illumina.","type_id":"1000452","type_name":"DNA Analysis Kit","type_desc":"A laboratory kit containing reagents and materials used to extract, purify, detect, measure, or otherwise evaluate genetic material from a sample.","type_acronym":""},{"_id":"1010338","name":"Qiagen DNeasy PowerBioFilm Kit","description":"Qiagen DNeasy PowerBioFilm Kit (Qiagen, Inc., Germantown, MD, 24000-50): DNA was extracted with the Qiagen DNeasy PowerBioFilm Kit (Qiagen, Inc., Germantown, MD, 24000-50).","type_id":"1000452","type_name":"DNA Analysis Kit","type_desc":"A laboratory kit containing reagents and materials used to extract, purify, detect, measure, or otherwise evaluate genetic material from a sample.","type_acronym":""},{"_id":"1010344","name":"Hammer and chisel","description":"Hammer and chisel: A hammer and chisel were used to collect coral samples.","type_id":"565","type_name":"Manual Biota Sampler","type_desc":"\"Manual Biota Sampler\" indicates that a sample was collected in situ by a person, possibly using a hand-held collection device such as a jar, a net, or their hands. This term could also refer to a simple tool like a hammer, saw, or other hand-held tool.","type_acronym":"Manual Biota Sampler"},{"_id":"1010343","name":"Qubit 2.0 fluorometer","description":"Qubit 2.0 fluorometer: DNA concentrations were measured with a Qubit 2.0 fluorometer.","type_id":"940036","type_name":"Qubit fluorometer","type_desc":"Benchtop fluorometer. The Invitrogen Qubit Fluorometer accurately and quickly measures the concentration of DNA, RNA, or protein in a single sample. It can also be used to assess RNA integrity and quality. \r\n\r\nManufactured by Invitrogen, Carlsbad, CA, USA (Invitrogen is one of several brands under the Thermo Fisher Scientific corporation.)","type_acronym":""},{"_id":"1010345","name":"SCUBA","description":"SCUBA: Coral samples were collected on SCUBA (self-contained underwater breathing apparatus).","type_id":"713363","type_name":"Self-Contained Underwater Breathing Apparatus","type_desc":"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.\r\n\r\nReference: https://oceanexplorer.noaa.gov/technology/technical/technical.html","type_acronym":"SCUBA"},{"_id":"1010346","name":"Polymerase chain reaction (PCR)","description":"PCR: Polymerase chain reaction (PCR) reactions were used to amplify 16S rRNA genes and ITS-2 rDNA.","type_id":"471582","type_name":"Thermal Cycler","type_desc":"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.\r\n\r\n(adapted from http://serc.carleton.edu/microbelife/research_methods/genomics/pcr.html)","type_acronym":"Thermal Cycler"},{"_id":"1010332","name":"120 kV JEOL JEM-1400Flash Transmission Electron Microscope","description":"120 kV JEOL JEM-1400Flash Transmission Electron Microscope equipped with a high-contrast pole piece and a 15 megapixel AMT NanoSprint15 sCMOS camera: Electron micrographs were captured with this technology.","type_id":"1010329","type_name":"Transmission Electron Microscope","type_desc":"An electron microscope that transmits a beam of electrons through a finely sliced section of a specimen and creates an image of the sample based on its effect on the phase of the electrons that pass through.","type_acronym":"TEM"}],"parameters":[{"_id":"1010351","name":"sample_id","format":"","frictionlessType":"string","description":"

Sequencing library ID

","units":{"_id":"","name":"unitless"},"type":{"_id":"960","name":"sample","description":"

unique sample identification or number; any combination of alpha numeric characters; precise definition is file dependent

"}},{"_id":"1010352","name":"coral_id","format":"","frictionlessType":"integer","description":"

ID of coral colony assigned at time of sampling

","units":{"_id":"","name":"unitless"},"type":{"_id":"960","name":"sample","description":"

unique sample identification or number; any combination of alpha numeric characters; precise definition is file dependent

"}},{"_id":"1010353","name":"col_health","format":"","frictionlessType":"string","description":"

Health of coral colony

","units":{"_id":"","name":"unitless"},"type":{"_id":"1741","name":"sample_descrip","description":"

text description or other traits of the sample collected

"}},{"_id":"1010354","name":"coral_species","format":"","frictionlessType":"string","description":"

Genus and species of the sampled coral

","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":"1010355","name":"coral_aphiaID","format":"","frictionlessType":"number","description":"

Aphia ID of the host (coral) species

","units":{"_id":"","name":"unitless"},"type":{"_id":"995","name":"taxon_code","description":"

taxonomic group or entity code, such as the AphiaID (from the World Register of Marine Species), NCBI taxon_id, or the ten digit number from the NODC Taxonomic List, v. 8.

"}},{"_id":"1010356","name":"collection_date","format":"%Y-%m-%d","frictionlessType":"date","description":"

Date collected

","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":"1010357","name":"site","format":"","frictionlessType":"string","description":"

The sampling site

","units":{"_id":"","name":"unitless"},"type":{"_id":"1124","name":"site","description":"

Sampling site identification.

"}},{"_id":"1010358","name":"buoy","format":"","frictionlessType":"number","description":"

The sampling buoy

","units":{"_id":"","name":"unitless"},"type":{"_id":"1684","name":"buoy_id","description":"

identification number or name of buoy

"}},{"_id":"1010359","name":"depth_ft","format":"","frictionlessType":"number","description":"

The sampling depth

","units":{"_id":"","name":"feet"},"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":"1010360","name":"latitude","format":"","frictionlessType":"number","description":"

The sampling latitude

","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":"1010362","name":"longitude","format":"","frictionlessType":"number","description":"

The sampling longitude

","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":"1010364","name":"ncbi_bioproject","format":"","frictionlessType":"string","description":"

The associated NCBI BioProject

","units":{"_id":"","name":"unitless"},"type":{"_id":"854958","name":"BioProject","description":"

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.

"}},{"_id":"1010365","name":"ncbi_biosample","format":"","frictionlessType":"string","description":"

The associated NCBI BioSample

","units":{"_id":"","name":"unitless"},"type":{"_id":"854959","name":"BioSample","description":"

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

"}},{"_id":"1010366","name":"ncbi_16S_sra","format":"","frictionlessType":"string","description":"

The associated NCBI SRA accession number for 16S data

","units":{"_id":"","name":"unitless"},"type":{"_id":"856986","name":"SRA_experiment","description":"

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

An Experiment is a consistent set of laboratory operations on input material with an expected result. It contains the metadata describing the library, platform selection, and processing parameters involved in a particular sequencing experiment.

The identifier usually begins with \"SRX\".

"}},{"_id":"1010367","name":"ncbi_ITS2_sra","format":"","frictionlessType":"string","description":"

The associated NCBI SRA accession number for ITS-2 data

","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":"1010368","name":"ncbi_RNAseq_sra","format":"","frictionlessType":"string","description":"

The associated NCBI SRA accession number for RNA-seq data

","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.

This identifier usually begins with SRR

"}},{"_id":"1010369","name":"TEM_file","format":"","frictionlessType":"string","description":"

The pdf file name of TEM images

","units":{"_id":"","name":"unitless"},"type":{"_id":"659543","name":"file_name","description":"

File name

"}},{"_id":"1010370","name":"histo_file","format":"","frictionlessType":"string","description":"

The pdf file name of histology images

","units":{"_id":"","name":"unitless"},"type":{"_id":"659543","name":"file_name","description":"

File name

"}}],"related_publications":[{"id":"737032","citation":"Apprill, A., McNally, S., Parsons, R., & Weber, L. (2015). Minor revision to V4 region SSU rRNA 806R gene primer greatly increases detection of SAR11 bacterioplankton. Aquatic Microbial Ecology, 75(2), 129–137. doi:10.3354/ame01753\r\n","relation_type":["Methods"],"relation_desc":""},{"id":"998005","citation":"Howe-Kerr, L. I., Knochel, A. M., Meyer, M. D., Sims, J. A., Karrick, C. E., Grupstra, C. G. B., Veglia, A. J., Thurber, A. R., Vega Thurber, R. L., & Correa, A. M. S. (2023). Filamentous virus-like particles are present in coral dinoflagellates across genera and ocean basins. The ISME Journal, 17(12), 2389–2402. https://doi.org/10.1038/s41396-023-01526-6\r\n","relation_type":["Methods"],"relation_desc":""},{"id":"996965","citation":"Hume, B. C. C., Ziegler, M., Poulain, J., Pochon, X., Romac, S., Boissin, E., de Vargas, C., Planes, S., Wincker, P., & Voolstra, C. R. (2018). An improved primer set and amplification protocol with increased specificity and sensitivity targeting the Symbiodinium ITS2 region. PeerJ, 6, e4816. Portico. https://doi.org/10.7717/peerj.4816\r\n","relation_type":["Methods"],"relation_desc":""},{"id":"748083","citation":"Kozich, J. J., Westcott, S. L., Baxter, N. T., Highlander, S. K., & Schloss, P. D. (2013). Development of a Dual-Index Sequencing Strategy and Curation Pipeline for Analyzing Amplicon Sequence Data on the MiSeq Illumina Sequencing Platform. Applied and Environmental Microbiology, 79(17), 5112–5120. doi:10.1128/aem.01043-13\r\n","relation_type":["Methods"],"relation_desc":""},{"id":"736995","citation":"Parada, A. E., Needham, D. M., & Fuhrman, J. A. (2015). Every base matters: assessing small subunit rRNA primers for marine microbiomes with mock communities, time series and global field samples. Environmental Microbiology, 18(5), 1403–1414. doi:10.1111/1462-2920.13023\r\n","relation_type":["Methods"],"relation_desc":""}],"related_datasets":[{"_id":"","name":"","url":"https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1292163/","relation_type":"IsRelatedTo","type_desc":"The dataset is related to another dataset.","relation_desc":"","citation":"Woods Hole Oceanographic Institution. Flower Garden Banks Reefs Pseudodiploria Strigosa disease. 2025/07. In: BioProject [Internet]. Bethesda, MD: National Library of Medicine (US), National Center for Biotechnology Information; 2011-. Available from: http://www.ncbi.nlm.nih.gov/bioproject/PRJNA1292163. NCBI:BioProject: PRJNA1292163."}],"services":[{"grouping":"","items":[{"name":"View Data","description":"An in-browser view of the primary tabular data file","url":"https://www.bco-dmo.org/dataset/1010240/data/view","contentType":"text/html","actionType":"view"}]},{"grouping":"ERDDAP","items":[{"name":"SUBSET DATA","description":"","url":"https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_1010240_v1.html","contentType":"text/html","actionType":"tool"},{"name":"VIEW TABLE","description":"","url":"https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_1010240_v1.htmlTable","contentType":"text/html","actionType":"view"},{"name":"CSV","description":"","url":"https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_1010240_v1.csv","contentType":"text/csv","actionType":"download"},{"name":"TSV","description":"","url":"https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_1010240_v1.tsv","contentType":"text/tsv","actionType":"download"},{"name":"GeoJSON","description":"","url":"https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_1010240_v1.geoJson","contentType":"application/geo+json","actionType":"download"},{"name":"MATLAB","description":"","url":"https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_1010240_v1.mat","contentType":"text/x-matlab","actionType":"download"},{"name":"netCDF","description":"","url":"https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_1010240_v1.nc","contentType":"application/x-netcdf","actionType":"download"}]},{"grouping":"Metadata","items":[{"name":"HTML","description":"A simple HTML page of the dataset metadata","url":"https://www.bco-dmo.org/dataset/1010240/description","contentType":"text/html","actionType":"view"},{"name":"PDF","description":"A PDF of the HTML dataset metadata","url":"https://www.bco-dmo.org/dataset/1010240/Dataset_description.pdf","contentType":"application/pdf","actionType":"download"},{"name":"ISO 19115-2 (NOAA Profile)","description":"","url":"https://www.bco-dmo.org/dataset/1010240/iso","contentType":"application/xml","actionType":"download"}]}],"programs":[],"projects":[{"_id":"889917","name":"Collaborative Research: RAPID: A multi-scale approach to predicting coral disease spread: leveraging an outbreak on coral-dense isolated reefs","acronym":"FGB Disease","description":"$17"}],"archives":[{"id_value":"10.26008/1912/bco-dmo.1010240.1","url":"https://doi.org/10.26008/1912/bco-dmo.1010240.1","date_assigned":"2026-10-21","version_date":"2026-10-20","archiver":"Woods Hole Oceanographic Institution (WHOI BCO-DMO)","archiver_id":"191"}],"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":5},"downloads":{"count":54}}}}]