http://lod.bco-dmo.org/id/dataset/997771
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
2026-04-30
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
NCBI Sequence Read Archive (SRA) accession numbers for raw fastq sequence files of ITS-2 amplicons collected from healthy and SCTLD-affected tissues of nine coral species in Florida, U.S.A. and the U.S. Virgin Islands from 2018-2020
2026-05-14
publication
2026-05-14
revision
Woods Hole Oceanographic Institution (WHOI BCO-DMO)
2026-05-14
publication
https://doi.org/10.26008/1912/bco-dmo.997771.1
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
Erinn M. Muller
Mote Marine Laboratory
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., Correa, A. M., Brandt, M., Apprill, A., Holstein, D., Mydlarz, L., Muller, E. M. (2026) NCBI Sequence Read Archive (SRA) accession numbers for raw fastq sequence files of ITS-2 amplicons collected from healthy and SCTLD-affected tissues of nine coral species in Florida, U.S.A. and the U.S. Virgin Islands from 2018-2020. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2026-05-14 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.997771.1 [access date]
SCTLD-associated Symbiodiniaceae ITS-2 Dataset Description: Methods and Sampling: <p>For samples collected from the Florida Keys, U.S.A., sterile, 10 milliliter (mL) syringes were used to scrape/remove tissue from <em>Montastraea cavernosa</em>, <em>Orbicella faveolata</em>, <em>Colpophyllia natans</em>, <em>Meandrina meandrites</em>, and <em>Pseudodiploria strigosa</em> corals. For <em>Siderastrea siderea</em> corals collected from the Florida Keys, U.S.A., a sterile corer was used to scrape tissue off, which was captured in a sterile syringe. Coral tissues were transferred from the syringes to plastic tubes before transport on ice to the South Florida Regional Laboratory of the Florida Fish &amp; Wildlife Conservation Commission's Fish and Wildlife Research Institute. There, coral tissues were flash frozen with liquid nitrogen before storage at -80 degrees Celsius (°C). DNA was extracted from samples using DNeasy PowerSoil Kits (QIAGEN, Germantown, MD, USA). 6 mL of coral tissue/mucus slurries were used for <em>S. siderea</em>, but 2 mL were used for all other species. Each slurry was centrifuged, and the supernatant was discarded to isolate a pellet of coral tissue/mucus. These methods are described by Clark et al. (2021).</p>
<p>For samples collected from the United States Virgin Islands, diseased and apparently healthy <em>Porites astreoides</em>, <em>M. cavernosa</em>, <em>Orbicella annularis</em>, <em>S. siderea</em>, <em>C. natans</em>, <em>Diploria labyrinthiformis</em>, <em>M. meandrites</em>, and <em>P. strigosa</em> corals were collected by divers on SCUBA via hammer and chisel. Fragments were stored in individual, sterile whirlpaks before being flash frozen in a charged liquid nitrogen dry shipper on the boat and subsequently stored at -80°C. All <em>in situ</em> samples (i.e., from both Florida, U.S.A., and the U.S. Virgin Islands) were sampled as sets of stony coral tissue loss disease-affected and apparently healthy conspecifics. Two samples were collected from each diseased coral: one adjacent to the gross tissue loss lesion and one from apparently healthy tissue on the same coral. One sample was collected from a nearby conspecific coral that was apparently healthy. Coral tissue was airbrushed from the flash-frozen fragments using phosphate buffered saline. Then, coral tissue slurry was centrifuged, and the supernatant was discarded to isolate a pellet of coral tissue/mucus. No more than 0.040 grams (g) of coral tissue was used for a DNA extraction using the ZymoBIOMICS DNA/RNA Miniprep Kit (ZymoResearch, Irvine, CA, USA).</p>
<p>Apparently healthy corals (<em>C. natans</em>, <em>M. cavernosa</em>, <em>O. annularis</em>, <em>P. astreoides</em>, <em>P. strigosa</em>, and <em>S. siderea</em>) for<em> </em>the stony coral tissue loss disease transmission experiment were originally collected from Rupert's Rock by divers on SCUBA via hammer and chisel. Corals were placed in separate, sealed bags before transport to the Center for Marine and Environmental Sciences in coolers with seawater. There, corals were halved with a sterilized chop saw or bandsaw and placed into shaded raceways for at least one week prior to the start of the experiment. One day before the start of the transmission experiment, healthy and diseased <em>Diploria labyrinthiformis</em> corals were collected from Rupert's Rock&nbsp;and Flat Cay, respectively, via hammer and chisel. These <em>D. labyrinthiformis</em> corals were placed in separate gallon bags and transported to the Center for Marine and Environmental Sciences. For the control treatment, one fragment each of <em>C. natans</em>, <em>M. cavernosa</em>, <em>O. annularis</em>, <em>P. astreoides</em>, <em>P. strigosa</em>, and <em>S. siderea</em> were randomly arranged around a central apparently healthy <em>D. labyrinthiformis</em> coral. For the disease treatment, corresponding fragments of each genet were randomly arranged around a central diseased <em>D. labyrinthiformis</em> coral. This was replicated eight times. Corals were examined twice daily. If a lesion was observed to actively expand for at least 12 hours, the fragment was removed from the experimental container and flash frozen in a charged dry shipper. After eight days, all remaining fragments were flash frozen. Methods for the transmission experiment are reported by Meiling et al. (2021), and DNA was extracted according to the <em>in situ</em> samples collected from the U.S. Virgin Islands, as described above.</p>
<p>The internal transcribed spacer-2 (ITS-2) region of Symbiodiniaceae rDNA was amplified from all extracted DNA using the SYM_Var primer pair (Hume et al., 2018): SYM_VAR_5.8SII (5'-GAATTGCAGAACTCCGTGAACC-3') and SYM_REV (5'-CGGGTTCWCTTGTYTGACTTCATGC-3'). PCR reagents included 2 microliters (µL) of DNA, 0.42 µL of forward and reverse primers, 15 µL of DNase/RNase-free water, and 17.5 µL of EconoTaq PLUS GREEN 2X Master Mix. After 10 minutes at 74°C, PCR conditions included 32 cycles of 94°C for 1 minute, 59°C for 1 minute, and 74°C for 2 minutes, followed by 74°C for 7 minutes. Sequencing was performed on an Illumina MiSeq PE300 platform at Oregon State University's Center for Quantitative Life Sciences (OSU CQLS, Corvallis, OR, USA). These methods are described by Karrick et al. (in review).</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
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
Erinn M. Muller
Mote Marine Laboratory
941-388-4441 x 310
1600 Ken Thompson Parkway
Sarasota
FL
34241
USA
emuller@mote.org
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
coral_id
sample_id
health
host_phylum
host_class
host_order
host_family
host_genus
host_species
susceptibility
location
sampletype
site
latitude
longitude
year
col_health
figure_sample_id
figure_coral_id
ncbi_bioproject
ncbi_biosample
AphiaID
Illumina MiSeq PE300
centrifuge
hammer and chisel
SCUBA
syringe
PCR
theme
None, User defined
sample identification
sample description
phylum
taxonomic class
order
family
genus
species_epithet
site
latitude
longitude
year
NCBI BioProject accession
NCBI BioSample accession
taxon_code
featureType
BCO-DMO Standard Parameters
Automated DNA Sequencer
Centrifuge
Manual Biota Sampler
Self-Contained Underwater Breathing Apparatus
syringe
Thermal Cycler
instrument
BCO-DMO Standard Instruments
otherRestrictions
otherRestrictions
Access Constraints: none. Use Constraints: Please follow guidelines at: http://www.bco-dmo.org/terms-use Distribution liability: Under no circumstances shall BCO-DMO be liable for any direct, incidental, special, consequential, indirect, or punitive damages that result from the use of, or the inability to use, the materials in this data submission. If you are dissatisfied with any materials in this data submission your sole and exclusive remedy is to discontinue use.
A multi-scale approach to predicting infectious multi-host disease spread in marine benthic communities
https://osprey.bco-dmo.org/project/877263
A multi-scale approach to predicting infectious multi-host disease spread in marine benthic communities
<p><em>NSF Award Abstract:</em><br />
Marine diseases have devastating impacts on ocean ecosystems and this work will directly examine the framework for understanding disease transmission in the ocean. A team of ecologists, ocean connectivity and disease modelers, microbiologists, and coral immunologists (from the University of Virgin Islands (UVI), Louisiana State University (LSU), Rice University, University of Texas-Arlington and the Woods Hole Oceanographic Institution) will develop a model that predicts transmission of a devastating Caribbean coral disease that has the potential to impact the economic value of coral reefs, including those located in the U.S. This project will support multidisciplinary field and laboratory research experiences of graduate students at multiple minority-serving institutions, and will provide undergraduate students with hands-on training in modeling, ecological and molecular analysis techniques. UVI and LSU are in EPSCoR jurisdictions and have diverse student bodies, including numerous under-represented minority (URM) students. The research team will collaboratively provide URM students with research experiences in STEM fields. Project findings will be broadly communicated through virtual public programming, and through the Virgin Islands Coral Disease Advisory Committee with updates on the vicoraldisease.org website. A coral disease response workshop for the U.S. Virgin Islands will also be held, in which project results will be presented and used to support disease response planning.</p>
<p>Over the last four decades, marine diseases have decimated ecosystem engineers in marine coastal ecosystems, including the rocky intertidal, seagrasses and coral reefs. The pathogens driving these diseases have frequently been challenging to isolate, characterize and confirm, in part because they affect multiple host species and can spread by ocean currents, as well as through individual contact. Here, we propose a multi-scale epidemic model for studying marine disease that addresses both within-host and within-patch disease dynamics, and explicitly acknowledges the dispersal of pathogens between populations. Our interdisciplinary research team of ecologists, connectivity and disease modelers, microbiologists, and coral immunologists will integrate the largest set of predictors of marine disease spread to date: individual host species traits that allow for disease resistance or susceptibility, local transmission within communities that may have unique community structure, and hydrodynamic connectivity among susceptible communities. Modeling will be supported with rich data sets of within- and among-patch population characteristics and disease dynamics as well as molecular data on species-level disease responses. This project will advance knowledge of infectious diseases by integrating multidimensional scales and differential host susceptibilities into existing epidemiological models. This model will particularly advance the framework for studying marine diseases and has the potential to elucidate the transmission properties of a devastating Caribbean coral disease (stony coral tissue loss disease) that fits the most confounding and notorious hallmarks of marine diseases: infection of multiple hosts by an elusive pathogen.</p>
<p>This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.</p>
Multi-scale multi-host disease spread
largerWorkCitation
project
eng; USA
oceans
-81.4095
-64.895336
18.279247
24.7329
2018-01-01
2020-12-31
United States Virgin Islands
0
BCO-DMO catalogue of parameters from NCBI Sequence Read Archive (SRA) accession numbers for raw fastq sequence files of ITS-2 amplicons collected from healthy and SCTLD-affected tissues of nine coral species in Florida, U.S.A. and the U.S. Virgin Islands from 2018-2020
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/998089.rdf
Name: sample
Units: unitless
Description: <p>Sequencing library ID</p>
http://lod.bco-dmo.org/id/dataset-parameter/998090.rdf
Name: coral_id
Units: unitless
Description: <p>ID of coral sampled assigned at the time of sampling</p>
http://lod.bco-dmo.org/id/dataset-parameter/998091.rdf
Name: sample_id
Units: unitless
Description: <p>ID of sample assigned at the time of sampling</p>
http://lod.bco-dmo.org/id/dataset-parameter/998092.rdf
Name: health
Units: unitless
Description: <p>Tissue health state, where "healthy" is a sample collected from an apparently healthy coral (HH), "unaffected" is a sample of apparently healthy tissue taken away from the disease lesion on a diseased coral (HD), and "diseased" is tissue taken adjacent to the disease lesion on a diseased coral (DD)</p>
http://lod.bco-dmo.org/id/dataset-parameter/998093.rdf
Name: host_phylum
Units: unitless
Description: <p>Phylum of the sampled coral</p>
http://lod.bco-dmo.org/id/dataset-parameter/998094.rdf
Name: host_class
Units: unitless
Description: <p>Class of the sampled coral</p>
http://lod.bco-dmo.org/id/dataset-parameter/998095.rdf
Name: host_order
Units: unitless
Description: <p>Order of the sampled coral</p>
http://lod.bco-dmo.org/id/dataset-parameter/998096.rdf
Name: host_family
Units: unitless
Description: <p>Family of the sampled coral</p>
http://lod.bco-dmo.org/id/dataset-parameter/998097.rdf
Name: host_genus
Units: unitless
Description: <p>Genus of the sampled coral</p>
http://lod.bco-dmo.org/id/dataset-parameter/998098.rdf
Name: host_species
Units: unitless
Description: <p>Species of the sampled coral</p>
http://lod.bco-dmo.org/id/dataset-parameter/998099.rdf
Name: susceptibility
Units: unitless
Description: <p>Stony coral tissue loss disease (SCTLD) susceptibility of the sampled coral, based on NOAA's 2018 case definition of the disease (high, moderate, low)</p>
http://lod.bco-dmo.org/id/dataset-parameter/998100.rdf
Name: location
Units: unitless
Description: <p>Sampling location, either Florida, USA, (FL), or the United States Virgin Islands (USVI)</p>
http://lod.bco-dmo.org/id/dataset-parameter/998101.rdf
Name: sampletype
Units: unitless
Description: <p>Whether the sample was collected in situ or ex situ, and the tissue health state (HH, HD, or DD)</p>
http://lod.bco-dmo.org/id/dataset-parameter/998102.rdf
Name: site
Units: unitless
Description: <p>The sampling site; NA = ex situ sample; blank = site information is unavailable. </p>
http://lod.bco-dmo.org/id/dataset-parameter/998103.rdf
Name: latitude
Units: decimal degrees
Description: <p>Latitude of the sampling site</p>
http://lod.bco-dmo.org/id/dataset-parameter/998104.rdf
Name: longitude
Units: decimal degrees
Description: <p>Longitude of the sampling site</p>
http://lod.bco-dmo.org/id/dataset-parameter/998105.rdf
Name: year
Units: unitless
Description: <p>The sampling year</p>
http://lod.bco-dmo.org/id/dataset-parameter/998106.rdf
Name: col_health
Units: unitless
Description: <p>Whether the sampled coral was apparently healthy or diseased</p>
http://lod.bco-dmo.org/id/dataset-parameter/998107.rdf
Name: figure_sample_id
Units: unitless
Description: <p>The sample ID used on the x-axis of supplemental figures in Karrick et al. (in review)</p>
http://lod.bco-dmo.org/id/dataset-parameter/998108.rdf
Name: figure_coral_id
Units: unitless
Description: <p>The coral ID used for faceting of supplemental figures in Karrick et al. (in review)</p>
http://lod.bco-dmo.org/id/dataset-parameter/998109.rdf
Name: ncbi_bioproject
Units: unitless
Description: <p>The NCBI BioProject the sample is associated with</p>
http://lod.bco-dmo.org/id/dataset-parameter/998110.rdf
Name: ncbi_biosample
Units: unitless
Description: <p>The NCBI BioSample the sample is associated with</p>
http://lod.bco-dmo.org/id/dataset-parameter/998111.rdf
Name: AphiaID
Units: unitless
Description: <p>Aphia ID of the host species</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.997771.1
download
onLine
dataset
<p>For samples collected from the Florida Keys, U.S.A., sterile, 10 milliliter (mL) syringes were used to scrape/remove tissue from <em>Montastraea cavernosa</em>, <em>Orbicella faveolata</em>, <em>Colpophyllia natans</em>, <em>Meandrina meandrites</em>, and <em>Pseudodiploria strigosa</em> corals. For <em>Siderastrea siderea</em> corals collected from the Florida Keys, U.S.A., a sterile corer was used to scrape tissue off, which was captured in a sterile syringe. Coral tissues were transferred from the syringes to plastic tubes before transport on ice to the South Florida Regional Laboratory of the Florida Fish &amp; Wildlife Conservation Commission's Fish and Wildlife Research Institute. There, coral tissues were flash frozen with liquid nitrogen before storage at -80 degrees Celsius (°C). DNA was extracted from samples using DNeasy PowerSoil Kits (QIAGEN, Germantown, MD, USA). 6 mL of coral tissue/mucus slurries were used for <em>S. siderea</em>, but 2 mL were used for all other species. Each slurry was centrifuged, and the supernatant was discarded to isolate a pellet of coral tissue/mucus. These methods are described by Clark et al. (2021).</p>
<p>For samples collected from the United States Virgin Islands, diseased and apparently healthy <em>Porites astreoides</em>, <em>M. cavernosa</em>, <em>Orbicella annularis</em>, <em>S. siderea</em>, <em>C. natans</em>, <em>Diploria labyrinthiformis</em>, <em>M. meandrites</em>, and <em>P. strigosa</em> corals were collected by divers on SCUBA via hammer and chisel. Fragments were stored in individual, sterile whirlpaks before being flash frozen in a charged liquid nitrogen dry shipper on the boat and subsequently stored at -80°C. All <em>in situ</em> samples (i.e., from both Florida, U.S.A., and the U.S. Virgin Islands) were sampled as sets of stony coral tissue loss disease-affected and apparently healthy conspecifics. Two samples were collected from each diseased coral: one adjacent to the gross tissue loss lesion and one from apparently healthy tissue on the same coral. One sample was collected from a nearby conspecific coral that was apparently healthy. Coral tissue was airbrushed from the flash-frozen fragments using phosphate buffered saline. Then, coral tissue slurry was centrifuged, and the supernatant was discarded to isolate a pellet of coral tissue/mucus. No more than 0.040 grams (g) of coral tissue was used for a DNA extraction using the ZymoBIOMICS DNA/RNA Miniprep Kit (ZymoResearch, Irvine, CA, USA).</p>
<p>Apparently healthy corals (<em>C. natans</em>, <em>M. cavernosa</em>, <em>O. annularis</em>, <em>P. astreoides</em>, <em>P. strigosa</em>, and <em>S. siderea</em>) for<em> </em>the stony coral tissue loss disease transmission experiment were originally collected from Rupert's Rock by divers on SCUBA via hammer and chisel. Corals were placed in separate, sealed bags before transport to the Center for Marine and Environmental Sciences in coolers with seawater. There, corals were halved with a sterilized chop saw or bandsaw and placed into shaded raceways for at least one week prior to the start of the experiment. One day before the start of the transmission experiment, healthy and diseased <em>Diploria labyrinthiformis</em> corals were collected from Rupert's Rock&nbsp;and Flat Cay, respectively, via hammer and chisel. These <em>D. labyrinthiformis</em> corals were placed in separate gallon bags and transported to the Center for Marine and Environmental Sciences. For the control treatment, one fragment each of <em>C. natans</em>, <em>M. cavernosa</em>, <em>O. annularis</em>, <em>P. astreoides</em>, <em>P. strigosa</em>, and <em>S. siderea</em> were randomly arranged around a central apparently healthy <em>D. labyrinthiformis</em> coral. For the disease treatment, corresponding fragments of each genet were randomly arranged around a central diseased <em>D. labyrinthiformis</em> coral. This was replicated eight times. Corals were examined twice daily. If a lesion was observed to actively expand for at least 12 hours, the fragment was removed from the experimental container and flash frozen in a charged dry shipper. After eight days, all remaining fragments were flash frozen. Methods for the transmission experiment are reported by Meiling et al. (2021), and DNA was extracted according to the <em>in situ</em> samples collected from the U.S. Virgin Islands, as described above.</p>
<p>The internal transcribed spacer-2 (ITS-2) region of Symbiodiniaceae rDNA was amplified from all extracted DNA using the SYM_Var primer pair (Hume et al., 2018): SYM_VAR_5.8SII (5'-GAATTGCAGAACTCCGTGAACC-3') and SYM_REV (5'-CGGGTTCWCTTGTYTGACTTCATGC-3'). PCR reagents included 2 microliters (µL) of DNA, 0.42 µL of forward and reverse primers, 15 µL of DNase/RNase-free water, and 17.5 µL of EconoTaq PLUS GREEN 2X Master Mix. After 10 minutes at 74°C, PCR conditions included 32 cycles of 94°C for 1 minute, 59°C for 1 minute, and 74°C for 2 minutes, followed by 74°C for 7 minutes. Sequencing was performed on an Illumina MiSeq PE300 platform at Oregon State University's Center for Quantitative Life Sciences (OSU CQLS, Corvallis, OR, USA). These methods are described by Karrick et al. (in review).</p>
Specified by the Principal Investigator(s)
<p>Sequencing was performed on an Illumina MiSeq PE300 platform at Oregon State University's Center for Quantitative Life Sciences (OSU CQLS, Corvallis, OR, USA) with the ITS-2 rDNA SYM_Var primer pair. Raw fastq files were then uploaded to NCBI's Sequence Read Archive (SRA) under BioProjects PRJNA955224, PRJNA1230223, and PRJNA1375785.</p>
<p>Note that BioProject PRJNA1375785 will be made publicly available on or before 2027-01-01.</p>
Specified by the Principal Investigator(s)
- Created a site list using the latitude and longitude coordinates from the data submitter.
- Imported the site list and the original data file, "metadata_sym_sctld_its2.csv", into the BCO-DMO system.
- Applied find/replace on "site" field, correcting spelling of "Perseverence" to "Perseverance".
- Joined the site list to the primary data file based on the site name, creating new columns for latitude and longitude.
- Applied conditional find/replace on row 27 only, replacing the value "z" in the site column with an empty/missing value. (This site name is unknown.)
- Saved the final file as "997771_v1_sctld-associated_symbiodiniaceae_its-2.csv".
Specified by BCO-DMO Data Managers
asNeeded
7.x-1.1
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
Illumina MiSeq PE300
Illumina MiSeq PE300
PI Supplied Instrument Name: Illumina MiSeq PE300 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.
centrifuge
centrifuge
PI Supplied Instrument Name: centrifuge 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.
hammer and chisel
hammer and chisel
PI Supplied Instrument Name: hammer and chisel 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/
SCUBA
SCUBA
PI Supplied Instrument Name: SCUBA 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
syringe
syringe
PI Supplied Instrument Name: syringe Instrument Name: syringe Instrument Short Name: Instrument Description: A device used to inject fluids into or withdraw them from something; consists of a hollow barrel fitted with a plunger and a hollow needle.
PCR
PCR
PI Supplied Instrument Name: PCR 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)