http://lod.bco-dmo.org/id/dataset/1010240
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
2026-10-19
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
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
2026-10-20
publication
2026-10-20
revision
Woods Hole Oceanographic Institution (WHOI BCO-DMO)
2026-10-21
publication
https://doi.org/10.26008/1912/bco-dmo.1010240.1
Amy Apprill
Woods Hole Oceanographic Institution
principalInvestigator
Marilyn Brandt
University of the Virgin Islands Center for Marine and Environmental Studies
principalInvestigator
Adrienne M.S. Correa
Rice University
principalInvestigator
Daniel Holstein
Louisiana State University
principalInvestigator
Laura Mydlarz
University of Texas at Arlington
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: 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]
FGB22 PSTR Coral Disease Microscopy & Omics Dataset Description: Methods and Sampling: <p><strong>Sample Collection:</strong><br />
Following the disease outbreak, fifteen samples of <em>Pseudodiploria strigosa</em> 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 <em>in situ</em> as sets of diseased and apparently healthy <em>P. strigosa</em>, 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.</p>
<p><strong>Transmission Electron Microscopy (TEM) Imaging:</strong><br />
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.</p>
<p><strong>Nucleic Acid Extraction and Sequencing:</strong><br />
Subsets of the fifteen <em>P. strigosa</em> 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 <em>P. strigosa</em> 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.</p>
<p>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 <em>Symbiodiniaceae</em> ITS-2 rDNA and 16S rRNA genes for bacteria/archaea, respectively.</p>
<p>To characterize <em>Symbiodiniaceae</em> composition, the ITS-2 region of <em>Symbiodiniaceae</em> 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.</p>
<p>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.</p>
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
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-2530272 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=2530272
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
Adrienne M.S. Correa
Rice University
amsc@berkeley.edu
pointOfContact
Daniel Holstein
Louisiana State University
NY
USA
daniel.holstein@stonybrook.edu
pointOfContact
Laura Mydlarz
University of Texas at Arlington
817-272-0397
501 S. Nedderman Dr. 337 Life Sciences Building
Arlington
TX
76013
United States
mydlarz@uta.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
sample_id
coral_id
col_health
coral_species
coral_aphiaID
collection_date
site
buoy
depth_ft
latitude
longitude
ncbi_bioproject
ncbi_biosample
ncbi_16S_sra
ncbi_ITS2_sra
ncbi_RNAseq_sra
TEM_file
histo_file
Airbrush
Illumina MiSeq
Illumina Novaseq 6000
Bone cutters
Centrifuge
MinElute PCR Purification Kit
Invitrogen RNAqueous Kit (AM1914)
Ambion DNase I (RNase-free) kit from Invitrogen (Life Technologies AM2222)
NEBNext Ultra II RNA Library Prep kit by Illumina
Qiagen DNeasy PowerBioFilm Kit
Hammer and chisel
Qubit 2.0 fluorometer
SCUBA
Polymerase chain reaction (PCR)
120 kV JEOL JEM-1400Flash Transmission Electron Microscope
theme
None, User defined
sample identification
sample description
species scientific name (binomial)
taxon_code
date
site
buoy_id
depth
latitude
longitude
NCBI BioProject accession
NCBI BioSample accession
NCBI SRA experiment accession (SRX)
NCBI SRA run accession (SRR)
file_name
featureType
BCO-DMO Standard Parameters
Airbrush
Automated DNA Sequencer
Automated DNA Sequencer
bone cutter
Centrifuge
DNA Analysis Kit
DNA Analysis Kit
DNA Analysis Kit
DNA Analysis Kit
DNA Analysis Kit
Manual Biota Sampler
Qubit fluorometer
Self-Contained Underwater Breathing Apparatus
Thermal Cycler
Transmission Electron Microscope
instrument
BCO-DMO Standard Instruments
FGB22
service
Deployment Activity
East and West Flower Garden Banks
place
Locations
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.
Collaborative Research: RAPID: A multi-scale approach to predicting coral disease spread: leveraging an outbreak on coral-dense isolated reefs
https://osprey.bco-dmo.org/project/889917
Collaborative Research: RAPID: A multi-scale approach to predicting coral disease spread: leveraging an outbreak on coral-dense isolated reefs
<p><em>NSF Award Abstract:</em></p>
<p>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.</p>
<p>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.</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>
FGB Disease
largerWorkCitation
project
eng; USA
oceans
East and West Flower Garden Banks
-93.814817
-93.597183
27.875317
27.9086
2022-09-20
2022-09-21
Flower Garden Banks National Marine Sanctuary, northwest Gulf of Mexico
0
BCO-DMO catalogue of parameters from 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)
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/1010351.rdf
Name: sample_id
Units: unitless
Description: <p>Sequencing library ID</p>
http://lod.bco-dmo.org/id/dataset-parameter/1010352.rdf
Name: coral_id
Units: unitless
Description: <p>ID of coral colony assigned at time of sampling</p>
http://lod.bco-dmo.org/id/dataset-parameter/1010353.rdf
Name: col_health
Units: unitless
Description: <p>Health of coral colony</p>
http://lod.bco-dmo.org/id/dataset-parameter/1010354.rdf
Name: coral_species
Units: unitless
Description: <p>Genus and species of the sampled coral</p>
http://lod.bco-dmo.org/id/dataset-parameter/1010355.rdf
Name: coral_aphiaID
Units: unitless
Description: <p>Aphia ID of the host (coral) species</p>
http://lod.bco-dmo.org/id/dataset-parameter/1010356.rdf
Name: collection_date
Units: unitless
Description: <p>Date collected</p>
http://lod.bco-dmo.org/id/dataset-parameter/1010357.rdf
Name: site
Units: unitless
Description: <p>The sampling site</p>
http://lod.bco-dmo.org/id/dataset-parameter/1010358.rdf
Name: buoy
Units: unitless
Description: <p>The sampling buoy</p>
http://lod.bco-dmo.org/id/dataset-parameter/1010359.rdf
Name: depth_ft
Units: feet
Description: <p>The sampling depth</p>
http://lod.bco-dmo.org/id/dataset-parameter/1010360.rdf
Name: latitude
Units: decimal degrees
Description: <p>The sampling latitude</p>
http://lod.bco-dmo.org/id/dataset-parameter/1010362.rdf
Name: longitude
Units: decimal degrees
Description: <p>The sampling longitude</p>
http://lod.bco-dmo.org/id/dataset-parameter/1010364.rdf
Name: ncbi_bioproject
Units: unitless
Description: <p>The associated NCBI BioProject</p>
http://lod.bco-dmo.org/id/dataset-parameter/1010365.rdf
Name: ncbi_biosample
Units: unitless
Description: <p>The associated NCBI BioSample</p>
http://lod.bco-dmo.org/id/dataset-parameter/1010366.rdf
Name: ncbi_16S_sra
Units: unitless
Description: <p>The associated NCBI SRA accession number for 16S data</p>
http://lod.bco-dmo.org/id/dataset-parameter/1010367.rdf
Name: ncbi_ITS2_sra
Units: unitless
Description: <p>The associated NCBI SRA accession number for ITS-2 data</p>
http://lod.bco-dmo.org/id/dataset-parameter/1010368.rdf
Name: ncbi_RNAseq_sra
Units: unitless
Description: <p>The associated NCBI SRA accession number for RNA-seq data</p>
http://lod.bco-dmo.org/id/dataset-parameter/1010369.rdf
Name: TEM_file
Units: unitless
Description: <p>The pdf file name of TEM images</p>
http://lod.bco-dmo.org/id/dataset-parameter/1010370.rdf
Name: histo_file
Units: unitless
Description: <p>The pdf file name of histology images</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
https://doi.org/10.26008/1912/bco-dmo.1010240.1
download
onLine
dataset
<p><strong>Sample Collection:</strong><br />
Following the disease outbreak, fifteen samples of <em>Pseudodiploria strigosa</em> 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 <em>in situ</em> as sets of diseased and apparently healthy <em>P. strigosa</em>, 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.</p>
<p><strong>Transmission Electron Microscopy (TEM) Imaging:</strong><br />
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.</p>
<p><strong>Nucleic Acid Extraction and Sequencing:</strong><br />
Subsets of the fifteen <em>P. strigosa</em> 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 <em>P. strigosa</em> 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.</p>
<p>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 <em>Symbiodiniaceae</em> ITS-2 rDNA and 16S rRNA genes for bacteria/archaea, respectively.</p>
<p>To characterize <em>Symbiodiniaceae</em> composition, the ITS-2 region of <em>Symbiodiniaceae</em> 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.</p>
<p>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.</p>
Specified by the Principal Investigator(s)
<p>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).</p>
Specified by the Principal Investigator(s)
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.
CURATION ACTIONS PERFORMED ON DATA
- Imported original file "FGB22_BCO-DMO_metadata_SRA.xlsx" (sheet 1) into the BCO-DMO data processing system.
- Treated "NA" as a missing value (Note: missing values are empty/blank in the final CSV file).
- Converted collection_date from format %d-%b-%y to format %Y-%m-%d.
- Saved the final file as "1010240_v1_fgb22_pstr_coral_disease.csv".
CURATION ACTIONS PERFORMED ON METADATA
- BCO-DMO's standard metadata entry and text formatting steps were performed. See: https://www.bco-dmo.org/how-to/standard-curation-edits
ISSUES POTENTIALLY IMPACTING REUSE
- N/A
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
Airbrush
Airbrush
PI Supplied Instrument Name: Airbrush PI Supplied Instrument Description:Airbrush: An airbrush was used to create coral tissue slurry for DNA extraction. Instrument Name: Airbrush Instrument Short Name:Airbrush Instrument Description: Device for spraying liquid by means of compressed air.
Illumina MiSeq
Illumina MiSeq
PI Supplied Instrument Name: Illumina MiSeq PI Supplied Instrument Description:Illumina MiSeq: 16S and ITS-2 sequencing was performed on an Illumina MiSeq platform (PE250 and PE300, respectively). 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.
Illumina Novaseq 6000
Illumina Novaseq 6000
PI Supplied Instrument Name: Illumina Novaseq 6000 PI Supplied Instrument Description:Illumina Novaseq 6000: RNA-seq was performed on an Illumina Novaseq 6000 platform. 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.
Bone cutters
Bone cutters
PI Supplied Instrument Name: Bone cutters PI Supplied Instrument Description:Bone cutters: Sterile bone cutters were used to scrape coral tissue for RNA extraction. Instrument Name: bone cutter Instrument Short Name: Instrument Description: A bone cutter is a surgical instrument used to cut bones or coral fragments.
Centrifuge
Centrifuge
PI Supplied Instrument Name: Centrifuge PI Supplied Instrument Description:Centrifuge: A 4°C centrifuge was used to create a pellet of coral tissue slurry. 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.
MinElute PCR Purification Kit
MinElute PCR Purification Kit
PI Supplied Instrument Name: MinElute PCR Purification Kit PI Supplied Instrument 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). Instrument Name: DNA Analysis Kit Instrument Short Name: Instrument Description: A laboratory kit containing reagents and materials used to extract, purify, detect, measure, or otherwise evaluate genetic material from a sample.
Invitrogen RNAqueous Kit (AM1914)
Invitrogen RNAqueous Kit (AM1914)
PI Supplied Instrument Name: Invitrogen RNAqueous Kit (AM1914) PI Supplied Instrument Description:Invitrogen RNAqueous Kit (AM1914): RNA was extracted with the Invitrogen RNAqueous Kit (AM1914). Instrument Name: DNA Analysis Kit Instrument Short Name: Instrument Description: A laboratory kit containing reagents and materials used to extract, purify, detect, measure, or otherwise evaluate genetic material from a sample.
Ambion DNase I (RNase-free) kit from Invitrogen (Life Technologies AM2222)
Ambion DNase I (RNase-free) kit from Invitrogen (Life Technologies AM2222)
PI Supplied Instrument Name: Ambion DNase I (RNase-free) kit from Invitrogen (Life Technologies AM2222) PI Supplied Instrument Description:Potential DNA and chromatin contamination was removed from each sample using the Ambion DNase I (RNase-free) kit from Invitrogen (Life Technologies AM2222). Instrument Name: DNA Analysis Kit Instrument Short Name: Instrument Description: A laboratory kit containing reagents and materials used to extract, purify, detect, measure, or otherwise evaluate genetic material from a sample.
NEBNext Ultra II RNA Library Prep kit by Illumina
NEBNext Ultra II RNA Library Prep kit by Illumina
PI Supplied Instrument Name: NEBNext Ultra II RNA Library Prep kit by Illumina PI Supplied Instrument 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. Instrument Name: DNA Analysis Kit Instrument Short Name: Instrument Description: A laboratory kit containing reagents and materials used to extract, purify, detect, measure, or otherwise evaluate genetic material from a sample.
Qiagen DNeasy PowerBioFilm Kit
Qiagen DNeasy PowerBioFilm Kit
PI Supplied Instrument Name: Qiagen DNeasy PowerBioFilm Kit PI Supplied Instrument 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). Instrument Name: DNA Analysis Kit Instrument Short Name: Instrument Description: A laboratory kit containing reagents and materials used to extract, purify, detect, measure, or otherwise evaluate genetic material from a sample.
Hammer and chisel
Hammer and chisel
PI Supplied Instrument Name: Hammer and chisel PI Supplied Instrument Description:Hammer and chisel: A hammer and chisel were used to collect coral samples. Instrument Name: Manual Biota Sampler Instrument Short Name:Manual Biota Sampler Instrument Description: "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. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/90/
Qubit 2.0 fluorometer
Qubit 2.0 fluorometer
PI Supplied Instrument Name: Qubit 2.0 fluorometer PI Supplied Instrument Description:Qubit 2.0 fluorometer: DNA concentrations were measured with a Qubit 2.0 fluorometer. Instrument Name: Qubit fluorometer Instrument Short Name: Instrument Description: 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.
Manufactured by Invitrogen, Carlsbad, CA, USA (Invitrogen is one of several brands under the Thermo Fisher Scientific corporation.)
SCUBA
SCUBA
PI Supplied Instrument Name: SCUBA PI Supplied Instrument Description:SCUBA: Coral samples were collected on SCUBA (self-contained underwater breathing apparatus). 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
Polymerase chain reaction (PCR)
Polymerase chain reaction (PCR)
PI Supplied Instrument Name: Polymerase chain reaction (PCR) PI Supplied Instrument Description:PCR: Polymerase chain reaction (PCR) reactions were used to amplify 16S rRNA genes and ITS-2 rDNA. 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)
120 kV JEOL JEM-1400Flash Transmission Electron Microscope
120 kV JEOL JEM-1400Flash Transmission Electron Microscope
PI Supplied Instrument Name: 120 kV JEOL JEM-1400Flash Transmission Electron Microscope PI Supplied Instrument 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. Instrument Name: Transmission Electron Microscope Instrument Short Name:TEM Instrument Description: 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.
Cruise: FGB22
FGB22
R/V Manta
R/V Manta
vessel
R/V Manta
R/V Manta
vessel