http://lod.bco-dmo.org/id/dataset/924594
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
2024-04-09
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
16S rRNA sequences for outplanted Acropora cervicornis sexual recruits collected from Mote Marine Laboratory and Looe Key National Marine Sanctuary from 2020-2022
2026-09-11
publication
2026-09-11
revision
Woods Hole Oceanographic Institution (WHOI BCO-DMO)
2026-09-11
publication
https://doi.org/10.26008/1912/bco-dmo.924594.1
Rebecca Vega Thurber
Oregon State University
principalInvestigator
Erinn M. Muller
Mote Marine Laboratory
principalInvestigator
Grace J. Klinges
Mote Marine Laboratory
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: Klinges, G. J., Muller, E. M., Vega Thurber, R. (2026) 16S rRNA sequences for outplanted Acropora cervicornis sexual recruits collected from Mote Marine Laboratory and Looe Key National Marine Sanctuary from 2020-2022. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2026-09-11 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.924594.1 [access date]
16S rRNA sequences for outplanted Acropora cervicornis sexual recruits Dataset Description: Methods and Sampling: <p>To sample each coral, 6-8 polyps&nbsp;were excised from outplanted corals using bone cutters and temporarily stored in individual Whirl-Paks on ice until reaching shore. Upon shore, samples were transferred from Whirl Parks using flame-sterilized tweezers placed in a 1.5mL microcentrifuge tube containing 1mL of DNA/RNA shield (Zymo Research, R1100-250, Irvine, CA, USA). Samples were transferred to a -80℃ freezer for long-term storage. In preparation for DNA extractions, the samples were removed from the -80℃ freezer and thawed on ice. With flame-sterilized tweezers, half of the biomass was transferred to a Disruptor Tube (Omega Bio-Tek, Norcross, GA, USA), the other half was kept as a bioarchive and returned to -80℃. DNA from each sample was isolated utilizing the E.Z.N.A.® Soil DNA Kit (Omega Bio-Tek, Norcross, GA, USA) with slight modifications to the manufacturer’s protocol to increase yield. DNA isolates were stored at -80℃. DNA quantity and quality was assessed utilizing a NanoDrop spectrophotometer (Thermo Fisher Scientific™, Waltham, MA, USA). Samples were submitted to MR DNA for 16S rRNA PCR amplification and sequencing (www.mrdnalab.com, Shallowater, TX, USA). Amplification of the 16S rRNA gene was conducted using the 515F-806R primer set, which targets the V4 region of the 16S rRNA, with barcodes on the forward primer&nbsp;(Apprill et al., 2015). The 16S rRNA gene V4 variable region was amplified via a 30-cycle PCR using the HotStarTaq Plus Master Mix Kit (Qiagen, Germantown, MD) under the following conditions: 95°C for 5 minutes, followed by 30 cycles of 95°C for 30 seconds, 53°C for 40 seconds and 72°C for 1 minute, after which a final elongation step at 72°C for 10 minutes was performed. After amplification, PCR products were checked in 2% agarose gel to determine the success of amplification and the relative intensity of bands. Samples were multiplexed using unique dual indices and were pooled together in equal proportions based on their molecular weight and DNA concentrations. Pooled samples were purified using calibrated Ampure XP beads (Beckman Coutler, CA, USA). Then the pooled and purified PCR product was used to prepare an Illumina DNA library. A PCR negative control was included in library preparation but did not produce a viable library. Paired-end sequencing was performed at MR DNA on an Illumina MiSeq following the manufacturer's guidelines.</p>
<p>Sampling locations:</p>
<p>- Mote's&nbsp;<em>in situ&nbsp;</em>nursery. Approximate central coordinate 24.56257, -81.40009.<br />
- Site in Looe Key National Marine Sanctuary: U-10, U-11, and U-12. Approximate central coordinate 24.54093, -81.43539.<br />
- Site in Looe Key National Marine Sanctuary:&nbsp;Unnamed site west of U-11. Approximate central coordinate 24.54069, -81.43652.</p>
<p>Samples collected under permit number FKNMS-2020-188</p>
<p>&nbsp;</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1923836 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1923836
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1923926 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1923926
completed
Rebecca Vega Thurber
Oregon State University
rvegathurber@gmail.com
pointOfContact
Erinn M. Muller
Mote Marine Laboratory
941-388-4441 x 310
1600 Ken Thompson Parkway
Sarasota
FL
34241
USA
emuller@mote.org
pointOfContact
Grace J. Klinges
Mote Marine Laboratory
Center for Global Discovery and Conservation Science
Tempe
AZ
USA
gklinges@asu.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
SampleName
Run
BioSample
Sample
SRAStudy
Experiment
Submission
BioProject
organism
TaxID
env_broad_scale
env_broad_scale_term
env_local_scale
env_local_scale_term
env_medium
host
geo_loc_name
lat
lon
collection_date
Family
geno_family
outplant_els_genotype
NCBI_genotype
timepoint
type
project
Location
Timepoint
location_time
timepoint_description
egg
sperm
rica
acquired_1yr
rica_time
acquired_time
days
cross
title
design_description
platform
instrument_model
LibraryName
LibraryStrategy
LibrarySource
LibrarySelection
LibraryLayout
filetype
filename
filename2
NanoDrop spectrophotometer
theme
None, User defined
sample identification
NCBI SRA run accession (SRR)
NCBI BioSample accession
NCBI SRA Sample accession (SRS)
NCBI SRA study accession (SRP)
NCBI SRA experiment accession (SRX)
accession number
NCBI BioProject accession
No BCO-DMO term
sample description
region
latitude
longitude
date
seq_descrip
instrument
instrument model
datatype
file_name
featureType
BCO-DMO Standard Parameters
Automated DNA Sequencer
bone cutter
Thermo Scientific NanoDrop spectrophotometer
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.
Collaborative Research: Tracking the interacting roles of the environment, host genotype, and a novel Rickettsiales in coral disease susceptibility
https://osprey.bco-dmo.org/project/820022
Collaborative Research: Tracking the interacting roles of the environment, host genotype, and a novel Rickettsiales in coral disease susceptibility
<p><em>NSF Award Abstract:</em><br />
Historically one of the most abundant reef-building corals in Florida and the wider Caribbean, the staghorn coral, <em>Acropora cervicornis</em>, is now listed as critically endangered primarily because of previous and reoccurring disease events. Understanding the holistic mechanisms of disease susceptibility in this coral is a top concern of practitioners engaged in conservation and restoration. The investigators recently discovered a group of parasitic bacteria common within the microbial community of <em>A. cervicornis</em> that can reduce the growth and health of corals when reefs are exposed to nutrient polluted waters. Determining how interactions among the coral host, this parasitic microbe, and the environment are linked to disease susceptibility provides critical insight and greater success of future restoration efforts. Yet the complexity of animal microbiomes and the contextual nature of disease make it difficult to identify the specific cause of many disease outbreaks. In this project, the investigators conduct experiments to explore the interactions among different genetic strains of coral and these bacteria in various nutrient scenarios to better understand how this bacterium affects the susceptibility of staghorn coral to diseases. This project also characterizes the genomics, host range, and local and global distribution of this bacterial coral parasite to determine how its evolutionary history and physiology drive disease susceptibility in this important coral species. The project trains two postdocs, one technician, and seven students (one graduate, six undergraduates) in integrative sciences that span marine science, physiology, genetics, microbiology, omics, and statistical modeling. A research-based after school program in Florida is expanded to include microbiology and create a new program module called Microbial warriors, with a focus on women in science. The investigators produce documentary style films and outreach materials to broadly communicate the project science and conservation efforts to local and national communities via presentations at Mote Marine Lab and the Oregon Museum of Science and Industry. This project is co-funded by the Biological Oceanography Program in the Division of Ocean Sciences and the Symbiosis, Defense, and Self-recognition Program in the Division of Integrative Organismal Systems.</p>
<p>The investigators recently identified a marine <em>Rickettsiales</em> bacterium that, in corals, can be stimulated to grow in the presence of elevated nitrogen and phosphorous species. Based on genomic reconstruction and phylogeography, this bacteria is classified as a novel bacterial genus, <em>Candidatus Aquarickettsia</em>, and showed that it is broadly associated with scleractinian corals worldwide. Importantly, using a model system, the endangered <em>Acropora cervicornis</em> coral, the team has also shown that the growth of this bacterium in vivo is associated with reduced host growth and increased disease susceptibility. This project aims to more completely evaluate the mechanisms behind and impacts of these inducible infections on coral physiology and host-bacterial symbiosis. The investigators conduct nutrient dosing experiments on different coral genotypes with various <em>Rickettsiales</em> abundances. Using a range of omics and microscopy techniques, the team quantifies the resulting effects on holobiont phenotypes. The investigators are also comparing the genomes of these bacteria in the different Acroporid hosts and other coral genera to evaluate facets of the bacterium's evolutionary history, as well as to identify possible mechanisms of its proliferation, virulence, and host specificity. This interdisciplinary project mechanistically links nutrients to temporal changes in host, algal symbiont, and bacterial parasite physiology and also explain why there is natural variation in these responses by exploring how host and parasite genotypes and growth dynamics combined with environmental contextuality alter holobiont phenotypes.</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>
Coral Rickettsiales
largerWorkCitation
project
eng; USA
oceans
-81.43652
-81.40009
24.54069
24.56257
2020-10-07
2022-04-21
at Oregon State University and in the Florida Keys at Mote Marine Laboratory
0
BCO-DMO catalogue of parameters from 16S rRNA sequences for outplanted Acropora cervicornis sexual recruits collected from Mote Marine Laboratory and Looe Key National Marine Sanctuary from 2020-2022
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
http://lod.bco-dmo.org/id/dataset-parameter/1007366.rdf
Name: SampleName
Units: unitless
Description: <p>Sample ID</p>
http://lod.bco-dmo.org/id/dataset-parameter/1007367.rdf
Name: Run
Units: unitless
Description: <p>The National Center for Biotechnology Information (NCBI) unique identifier assigned to a specific sequencing run results within a dataset</p>
http://lod.bco-dmo.org/id/dataset-parameter/1007368.rdf
Name: BioSample
Units: unitless
Description: <p>The National Center for Biotechnology Information (NCBI) BioSample accession number in the BioSample database.</p>
http://lod.bco-dmo.org/id/dataset-parameter/1007369.rdf
Name: Sample
Units: unitless
Description: <p>The National Center for Biotechnology Information (NCBI) sample identifier</p>
http://lod.bco-dmo.org/id/dataset-parameter/1007370.rdf
Name: SRAStudy
Units: unitless
Description: <p>The National Center for Biotechnology Information (NCBI) unique identifier assigned to a study</p>
http://lod.bco-dmo.org/id/dataset-parameter/1007371.rdf
Name: Experiment
Units: unitless
Description: <p>The National Center for Biotechnology Information (NCBI) unique identifier for an SRA experiment</p>
http://lod.bco-dmo.org/id/dataset-parameter/1007372.rdf
Name: Submission
Units: unitless
Description: <p>The National Center for Biotechnology Information (NCBI) unique identifier for sequencing data</p>
http://lod.bco-dmo.org/id/dataset-parameter/1007373.rdf
Name: BioProject
Units: unitless
Description: <p>The National Center for Biotechnology Information (NCBI) BioProject identifier.</p>
http://lod.bco-dmo.org/id/dataset-parameter/1007374.rdf
Name: organism
Units: unitless
Description: <p>Coral metagenome, a collection of genomes from many individuals within an environment or sample</p>
http://lod.bco-dmo.org/id/dataset-parameter/1007375.rdf
Name: TaxID
Units: unitless
Description: <p>description</p>
http://lod.bco-dmo.org/id/dataset-parameter/1007376.rdf
Name: env_broad_scale
Units: unitless
Description: <p>The National Center for Biotechnology Information (NCBI) environment identifier: terms that identify the major environment type(s) where your sample was collected</p>
http://lod.bco-dmo.org/id/dataset-parameter/1007377.rdf
Name: env_broad_scale_term
Units: unitless
Description: <p>The National Center for Biotechnology Information (NCBI) environment identifier term name: terms that identify the major environment type(s) where your sample was collected</p>
http://lod.bco-dmo.org/id/dataset-parameter/1007378.rdf
Name: env_local_scale
Units: unitless
Description: <p>The National Center for Biotechnology Information (NCBI) environment identifier: terms that identify environmental entities having causal influences upon the entity at time of sampling</p>
http://lod.bco-dmo.org/id/dataset-parameter/1007379.rdf
Name: env_local_scale_term
Units: unitless
Description: <p>The National Center for Biotechnology Information (NCBI) environment identifier term name: terms that identify environmental entities having causal influences upon the entity at time of sampling</p>
http://lod.bco-dmo.org/id/dataset-parameter/1007380.rdf
Name: env_medium
Units: unitless
Description: <p>The National Center for Biotechnology Information (NCBI) term that identifies the material displaced by the entity at time of sampling</p>
http://lod.bco-dmo.org/id/dataset-parameter/1007381.rdf
Name: host
Units: unitless
Description: <p>Animal host</p>
http://lod.bco-dmo.org/id/dataset-parameter/1007382.rdf
Name: geo_loc_name
Units: unitless
Description: <p>sampling location, geographic location of the origin of the sample</p>
http://lod.bco-dmo.org/id/dataset-parameter/1007383.rdf
Name: lat
Units: decimal degrees
Description: <p>Latitude of sampling location, south is negative</p>
http://lod.bco-dmo.org/id/dataset-parameter/1007385.rdf
Name: lon
Units: decimal degrees
Description: <p>Longitude of sampling location, west is negative</p>
http://lod.bco-dmo.org/id/dataset-parameter/1007387.rdf
Name: collection_date
Units: unitless
Description: <p>Collection date of organism</p>
http://lod.bco-dmo.org/id/dataset-parameter/1007388.rdf
Name: Family
Units: unitless
Description: <p>description</p>
http://lod.bco-dmo.org/id/dataset-parameter/1007389.rdf
Name: geno_family
Units: unitless
Description: <p>description</p>
http://lod.bco-dmo.org/id/dataset-parameter/1007390.rdf
Name: outplant_els_genotype
Units: unitless
Description: <p>description</p>
http://lod.bco-dmo.org/id/dataset-parameter/1007391.rdf
Name: NCBI_genotype
Units: unitless
Description: <p>description</p>
http://lod.bco-dmo.org/id/dataset-parameter/1007392.rdf
Name: timepoint
Units: unitless
Description: <p>description</p>
http://lod.bco-dmo.org/id/dataset-parameter/1007393.rdf
Name: type
Units: unitless
Description: <p>description</p>
http://lod.bco-dmo.org/id/dataset-parameter/1007394.rdf
Name: project
Units: unitless
Description: <p>description</p>
http://lod.bco-dmo.org/id/dataset-parameter/1007395.rdf
Name: Location
Units: unitless
Description: <p>description</p>
http://lod.bco-dmo.org/id/dataset-parameter/1007396.rdf
Name: Timepoint
Units: unitless
Description: <p>description</p>
http://lod.bco-dmo.org/id/dataset-parameter/1007397.rdf
Name: location_time
Units: unitless
Description: <p>description</p>
http://lod.bco-dmo.org/id/dataset-parameter/1007398.rdf
Name: timepoint_description
Units: unitless
Description: <p>description</p>
http://lod.bco-dmo.org/id/dataset-parameter/1007399.rdf
Name: egg
Units: unitless
Description: <p>description</p>
http://lod.bco-dmo.org/id/dataset-parameter/1007400.rdf
Name: sperm
Units: unitless
Description: <p>description</p>
http://lod.bco-dmo.org/id/dataset-parameter/1007401.rdf
Name: rica
Units: unitless
Description: <p>description</p>
http://lod.bco-dmo.org/id/dataset-parameter/1007402.rdf
Name: acquired_1yr
Units: unitless
Description: <p>description</p>
http://lod.bco-dmo.org/id/dataset-parameter/1007403.rdf
Name: rica_time
Units: unitless
Description: <p>description</p>
http://lod.bco-dmo.org/id/dataset-parameter/1007404.rdf
Name: acquired_time
Units: unitless
Description: <p>description</p>
http://lod.bco-dmo.org/id/dataset-parameter/1007405.rdf
Name: days
Units: unitless
Description: <p>description</p>
http://lod.bco-dmo.org/id/dataset-parameter/1007406.rdf
Name: cross
Units: unitless
Description: <p>description</p>
http://lod.bco-dmo.org/id/dataset-parameter/1007407.rdf
Name: title
Units: unitless
Description: <p>Library title</p>
http://lod.bco-dmo.org/id/dataset-parameter/1007408.rdf
Name: design_description
Units: unitless
Description: <p>Description explaining how this library was prepared and sequenced</p>
http://lod.bco-dmo.org/id/dataset-parameter/1007409.rdf
Name: platform
Units: unitless
Description: <p>Sequencing platform manufacturer</p>
http://lod.bco-dmo.org/id/dataset-parameter/1007410.rdf
Name: instrument_model
Units: unitless
Description: <p>Sequencer model</p>
http://lod.bco-dmo.org/id/dataset-parameter/1007411.rdf
Name: LibraryName
Units: unitless
Description: <p>Unique identifier for the sequencing library (can be the sample name repeated).</p>
http://lod.bco-dmo.org/id/dataset-parameter/1007412.rdf
Name: LibraryStrategy
Units: unitless
Description: <p>Sequencing library strategy</p>
http://lod.bco-dmo.org/id/dataset-parameter/1007413.rdf
Name: LibrarySource
Units: unitless
Description: <p>Source of sequencing library</p>
http://lod.bco-dmo.org/id/dataset-parameter/1007414.rdf
Name: LibrarySelection
Units: unitless
Description: <p>Selection used for sequencing library</p>
http://lod.bco-dmo.org/id/dataset-parameter/1007415.rdf
Name: LibraryLayout
Units: unitless
Description: <p>single or paired end sequencing reads</p>
http://lod.bco-dmo.org/id/dataset-parameter/1007416.rdf
Name: filetype
Units: unitless
Description: <p>File type</p>
http://lod.bco-dmo.org/id/dataset-parameter/1007417.rdf
Name: filename
Units: unitless
Description: <p>Forward reads file name</p>
http://lod.bco-dmo.org/id/dataset-parameter/1007418.rdf
Name: filename2
Units: unitless
Description: <p>Reverse reads file name</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.924594.1
download
onLine
dataset
<p>To sample each coral, 6-8 polyps&nbsp;were excised from outplanted corals using bone cutters and temporarily stored in individual Whirl-Paks on ice until reaching shore. Upon shore, samples were transferred from Whirl Parks using flame-sterilized tweezers placed in a 1.5mL microcentrifuge tube containing 1mL of DNA/RNA shield (Zymo Research, R1100-250, Irvine, CA, USA). Samples were transferred to a -80℃ freezer for long-term storage. In preparation for DNA extractions, the samples were removed from the -80℃ freezer and thawed on ice. With flame-sterilized tweezers, half of the biomass was transferred to a Disruptor Tube (Omega Bio-Tek, Norcross, GA, USA), the other half was kept as a bioarchive and returned to -80℃. DNA from each sample was isolated utilizing the E.Z.N.A.® Soil DNA Kit (Omega Bio-Tek, Norcross, GA, USA) with slight modifications to the manufacturer’s protocol to increase yield. DNA isolates were stored at -80℃. DNA quantity and quality was assessed utilizing a NanoDrop spectrophotometer (Thermo Fisher Scientific™, Waltham, MA, USA). Samples were submitted to MR DNA for 16S rRNA PCR amplification and sequencing (www.mrdnalab.com, Shallowater, TX, USA). Amplification of the 16S rRNA gene was conducted using the 515F-806R primer set, which targets the V4 region of the 16S rRNA, with barcodes on the forward primer&nbsp;(Apprill et al., 2015). The 16S rRNA gene V4 variable region was amplified via a 30-cycle PCR using the HotStarTaq Plus Master Mix Kit (Qiagen, Germantown, MD) under the following conditions: 95°C for 5 minutes, followed by 30 cycles of 95°C for 30 seconds, 53°C for 40 seconds and 72°C for 1 minute, after which a final elongation step at 72°C for 10 minutes was performed. After amplification, PCR products were checked in 2% agarose gel to determine the success of amplification and the relative intensity of bands. Samples were multiplexed using unique dual indices and were pooled together in equal proportions based on their molecular weight and DNA concentrations. Pooled samples were purified using calibrated Ampure XP beads (Beckman Coutler, CA, USA). Then the pooled and purified PCR product was used to prepare an Illumina DNA library. A PCR negative control was included in library preparation but did not produce a viable library. Paired-end sequencing was performed at MR DNA on an Illumina MiSeq following the manufacturer's guidelines.</p>
<p>Sampling locations:</p>
<p>- Mote's&nbsp;<em>in situ&nbsp;</em>nursery. Approximate central coordinate 24.56257, -81.40009.<br />
- Site in Looe Key National Marine Sanctuary: U-10, U-11, and U-12. Approximate central coordinate 24.54093, -81.43539.<br />
- Site in Looe Key National Marine Sanctuary:&nbsp;Unnamed site west of U-11. Approximate central coordinate 24.54069, -81.43652.</p>
<p>Samples collected under permit number FKNMS-2020-188</p>
<p>&nbsp;</p>
Specified by the Principal Investigator(s)
<p>No processing was performed on raw reads after sequencing before submission to NCBI.</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
- Created summary table of NCBI files
- Imported all tables, treating "", nd and NA as missing values.
- Merged all tables, removing duplicate columns. Joins based on the sample/BioSample identifiers: BioSample↔biosample_accession, SampleName↔sample_name, LibraryName↔sample_id
- Renamed the two conflicting genotype columns to outplant_els_genotype and NCBI_genotype
- Removed emptyRemoved empty, constant-valued (with value "new"), and redundant file-pointer columns and redundant file-pointer columns
- Added plain-language equivalents of the ENVO environment ontology codes.
- Split latitude & longitude values into a separate column, made west values negative
- Replaced special characters, spaces and periods from parameter names with underscores
- Standardized dates: zero-padded days, expanded 2-digit years, converted to ISO format yyyy-mm-dd
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
- NCBI BioProject PRJNA1023616 was recorded as a related resource.
ISSUES POTENTIALLY IMPACTING REUSE
- The submitted text used 'Aquarickettsia rohweri'. Proposed to change this to 'Candidatus Aquarickettsia rohweri' to match NCBI Taxonomy (taxid 2602574), under which the dataset's sequence accessions are registered.
- Parameter descriptions were not supplied. Inferred descriptions for all parameters where possible
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
PI Supplied Instrument Name: PI Supplied Instrument Description:Illumina MiSeq 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.
PI Supplied Instrument Name: Instrument Name: bone cutter Instrument Short Name: Instrument Description: A bone cutter is a surgical instrument used to cut bones or coral fragments.
NanoDrop spectrophotometer
NanoDrop spectrophotometer
PI Supplied Instrument Name: NanoDrop spectrophotometer Instrument Name: Thermo Scientific NanoDrop spectrophotometer Instrument Short Name:NanoDrop spectrophotometer Instrument Description: Thermo Scientific NanoDrop spectrophotometers provide microvolume quantification and purity assessments of DNA, RNA, and protein samples. NanoDrop spectrophotometers work on the principle of ultraviolet-visible spectrum (UV-Vis) absorbance. The range consists of the NanoDrop One/OneC UV-Vis Spectrophotometers, NanoDrop Eight UV-Vis Spectrophotometer and NanoDrop Lite Plus UV Spectrophotometer.