http://lod.bco-dmo.org/id/dataset/1003894
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
2026-08-06
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Sequence metadata for all sampled oysters from an experimental oyster reef restoration in Ninigret Pond, Rhode Island (USA) in 2017-2020
2026-08-07
publication
2026-08-07
revision
BCO-DMO Linked Data URI
2026-08-07
creation
http://lod.bco-dmo.org/id/dataset/1003894
A. Randall Hughes
Northeastern University
principalInvestigator
Sarit Truskey
Northeastern University
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: Hughes, A. R., Truskey, S. (2026) Sequence metadata for all sampled oysters from an experimental oyster reef restoration in Ninigret Pond, Rhode Island (USA) in 2017-2020. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2026-08-07 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/1003894 [access date]
Sequence metadata hatchery and restored reef oysters 2017-2020 Dataset Description: Methods and Sampling: <p>These data were published in Truskey et al. 2025 (Evolutionary Applications). All figure numbers and supplementary materials mentioned refer to Truskey et al. 2025 (Evolutionary Applications).</p>
<p><strong>Restoration experiment and sample collection</strong></p>
<p>In April 2017, we collaborated with local oyster farmers to source oyster eyed-larvae from four commercial hatcheries for the construction of new experimental oyster reefs in Ninigret Pond (Charlestown, Rhode Island, USA). Hatchery sources were selected across a broad geographic sampling range to maximize diversity (Figure&nbsp;1a of Truskey et al. 2025). They included two regional hatcheries, one from Massachusetts (MA) and one from New York (NY), and two more distant hatcheries, one from Maine (ME) and one from Virginia (VA). A local Rhode Island hatchery facility received oyster eyed-larvae from each source hatchery, set the eyed-larvae on dead oyster and/or clam shell (hereafter referred to as spat-on-shell oysters), and distributed the spat-on-shell oysters to three local oyster growers (Grower 1: MA; Grower 2: ME, NY, VA; Grower 3: NY, VA) who maintained these juvenile oysters on separate leased oyster farm plots prior to reef construction. Immediately prior to reef construction, we collected 20 juvenile spat-on-shell oysters from each grower-hatchery source combination for genetic analysis (<em>n</em> = 6 combinations; Grower 1-MA; Grower 2-ME; Grower 2-NY; Grower 2-VA; Grower 3-NY; Grower 3-VA).</p>
<p>In October and November 2017, we constructed 16 subtidal reefs within a no-harvest Shellfish Management Area in Ninigret Pond. Reefs were created across four 0.025-acre experimental blocks, with four reefs per block (Figure&nbsp;2 of Truskey et al. 2025). Each reef consisted of a base layer of 0.25 cubic yards of dead oyster or clam shell deployed in October and topped with 1.25 cubic yards of spat-on-shell oysters in early November from the stock grown out by the local oyster growers. Our experiment was originally designed to seed three reefs per block with a different single hatchery source from the four available hatchery sources and to seed the fourth reef per block with a mixed combination of the three sources (e.g., Reef 1: ME, Reef 2: MA, Reef 3: NY, Reef 4: ME+MA+NY). However, analysis of the hatchery samples from oyster growers collected prior to reef construction revealed an early, unintended mixing of some of the sources (Appendix&nbsp;S1 of Truskey et al. 2025; Figure&nbsp;S1 of Truskey et al. 2025), resulting in mixtures of multiple sources on 12 out of the 16 constructed reefs. Thus, we focused our analyses on the actual genetic composition of each reef as determined by genetic sampling at two time points (fall 2018, fall 2020).&nbsp;</p>
<p>In fall 2018, we haphazardly sampled live oysters from each reef on scuba or snorkel (<em>N</em> = 512 individuals total, 32 per reef). Oysters were put on ice and transported to the Northeastern University Marine Science Center where they were held at −80°C until DNA extraction. By the fall of 2020, live oyster densities on all experimental reefs had declined, reflecting mortality of the original planted oysters and a lack of recruitment, consistent with other data from this system (Barrett et&nbsp;al.&nbsp;2024). To assess whether this mortality was associated with a consistent change in the genetic composition of surviving oysters on reefs, we repeated our sampling in fall 2020 and compared the resulting reef genetic profiles to those from fall 2018. Reef sample sizes varied at this time point due to low live abundances (<em>N</em> = 249 individuals total, ranging from 8 to 32 per reef).</p>
<p><strong>DNA extraction, RADseq library preparation, and bioinformatics</strong></p>
<p>Genomic DNA was extracted using the E-Z 96 Tissue DNA Kit (Omega-Biotek, Norcross, GA) following the animal tissue protocol with tissue centrifugation. Double-digest restriction-site-associated DNA (ddRAD) libraries with individually barcoded samples were prepared in three batches following Parchman et al. (2012): (1) initial hatchery samples (n = 120), (2) fall 2018 reef samples (n = 480; 30 oysters per reef across 16 reefs), and (3) fall 2020 reef samples (n = 248). For additional details on ddRAD library preparation, see Appendix S2 of Truskey et al. 2025. All libraries were sequenced with 100-bp single-end reads on an Illumina platform. The initial and fall 2020 batches were sequenced on a single lane of the Illumina HiSeq 2500 at Tufts University Core Facility Genomics; the fall 2018 batch was sequenced on two lanes of the Illumina NovaSeq 6000 at the University of Texas at Austin Genomic Sequencing and Analysis Facility.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1652320 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1652320
onGoing
A. Randall Hughes
Northeastern University
781-581-7370
430 Nahant Rd.
Nahant
MA
01908
USA
ann.hughes@northeastern.edu
pointOfContact
Sarit Truskey
Northeastern University
240-205-3117
sbtruskey@gmail.com
pointOfContact
asNeeded
Dataset Version: 1
Unknown
sample_name
tissue
acc
assay_type
batch
bioproject
biosample
biosamplemodel
SRS
datastore_filetype
datastore_provider
datastore_region
experiment
genotyped_individual
collection_date
geo_loc_name_country
geo_loc_name_country_continent
geo_loc_name
latitude
longitude
isolate
isolation_source
instrument
libraryselection
librarysource
organism
platform
releasedate
primary_genetic_assignment
excluded_from_reeflevel_analyses
Title
Illumina HiSeq 2500
Illumina NovaSeq 6000
scuba
theme
None, User defined
sample identification
sample description
NCBI SRA run accession (SRR)
seq_descrip
NCBI BioProject accession
NCBI BioSample accession
NCBI SRA Sample accession (SRS)
NCBI SRA experiment accession (SRX)
date
region
latitude
longitude
site description
instrument
species scientific name (binomial)
platform
ISO_DateTime_UTC
flag
featureType
BCO-DMO Standard Parameters
Automated DNA Sequencer
Automated DNA Sequencer
Manual Biota Sampler
Self-Contained Underwater Breathing Apparatus
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.
CAREER: Linking genetic diversity, population density, and disease prevalence in seagrass and oyster ecosystems
https://osprey.bco-dmo.org/project/709942
CAREER: Linking genetic diversity, population density, and disease prevalence in seagrass and oyster ecosystems
<p><em>NSF Award Abstract:</em><br />
Disease outbreaks in the ocean are increasing, causing losses of ecologically important marine species, but the factors contributing to these outbreaks are not well understood. This 5-year CAREER project will study disease prevalence and intensity in two marine foundation species - the seagrass Zostera marina and the Eastern oyster Crassostrea virginica. More specifically, host-disease relationships will be explored to understand how genetic diversity and population density of the host species impacts disease transmission and risk. This work will pair large-scale experimental restorations and smaller-scale field experiments to examine disease-host relationships across multiple spatial scales. Comparisons of patterns and mechanisms across the two coastal systems will provide an important first step towards identifying generalities in the diversity-density-disease relationship. To enhance the broader impacts and utility of this work, the experiments will be conducted in collaboration with restoration practitioners and guided by knowledge ascertained from key stakeholder groups. The project will support the development of an early career female researcher and multiple graduate and undergraduate students. Students will be trained in state-of-the-art molecular techniques to quantify oyster and seagrass parasites. Key findings from the surveys and experimental work will be incorporated into undergraduate courses focused on Conservation Biology, Marine Biology, and Disease Ecology. Finally, students in these courses will help develop social-ecological surveys and mutual learning games to stimulate knowledge transfer with stakeholders through a series of workshops.</p>
<p>The relationship between host genetic diversity and disease dynamics is complex. In some cases, known as a dilution effect, diversity reduces disease transmission and risk. However, the opposite relationship, known as the amplification effect, can also occur when diversity increases the risk of infection. Even if diversity directly reduces disease risk, simultaneous positive effects of diversity on host density could lead to amplification by increasing disease transmission between infected and uninfected individuals. Large-scale field restorations of seagrasses (Zostera marina) and oysters (Crassostrea virginica) will be utilized to test the effects of host genetic diversity on host population density and disease prevalence/intensity. Additional field experiments independently manipulating host genetic diversity and density will examine the mechanisms leading to dilution or amplification. Conducting similar manipulations in two marine foundation species - one a clonal plant and the other a non-clonal animal - will help identify commonalities in the diversity-density-disease relationship. Further, collaborations among project scientists, students, and stakeholders will enhance interdisciplinary training and help facilitate the exchange of information to improve management and restoration efforts. As part of these efforts, targeted surveys will be used to document the perceptions and attitudes of managers and restoration practitioners regarding genetic diversity and its role in ecological resilience and restoration.</p>
Seagrass and Oyster Ecosystems
largerWorkCitation
project
eng; USA
biota
oceans
-71.6929
-71.6929
41.3549
41.3549
2017-11-07
2020-10-07
Coastal New England
0
BCO-DMO catalogue of parameters from Sequence metadata for all sampled oysters from an experimental oyster reef restoration in Ninigret Pond, Rhode Island (USA) in 2017-2020
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/1004082.rdf
Name: sample_name
Units: unitless
Description: <p>Name of the sample</p>
http://lod.bco-dmo.org/id/dataset-parameter/1004083.rdf
Name: tissue
Units: unitless
Description: <p>Type of tissue the sample was taken from</p>
http://lod.bco-dmo.org/id/dataset-parameter/1004084.rdf
Name: acc
Units: unitless
Description: <p>SRA Run accession in the form of SRR######## (ERR or DRR for INSDC partners)</p>
http://lod.bco-dmo.org/id/dataset-parameter/1004085.rdf
Name: assay_type
Units: unitless
Description: <p>Type of library (i.e. AMPLICON, RNA-Seq, WGS, etc)</p>
http://lod.bco-dmo.org/id/dataset-parameter/1004086.rdf
Name: batch
Units: unitless
Description: <p>RADseq library batch in which an individual was processed and sequenced</p>
http://lod.bco-dmo.org/id/dataset-parameter/1004087.rdf
Name: bioproject
Units: unitless
Description: <p>BioProject accession in the form of PRJNA######## (PRJEB####### or PRJDB###### for INSDC partners)</p>
http://lod.bco-dmo.org/id/dataset-parameter/1004088.rdf
Name: biosample
Units: unitless
Description: <p>BioSample accession in the form of SAMN######## (SAMEA##### or SAMD##### for INSDC partners)</p>
http://lod.bco-dmo.org/id/dataset-parameter/1004089.rdf
Name: biosamplemodel
Units: unitless
Description: <p>The BioSample package/model that was picked</p>
http://lod.bco-dmo.org/id/dataset-parameter/1004090.rdf
Name: SRS
Units: unitless
Description: <p>NCBI SRA Sample accession (SRS)</p>
http://lod.bco-dmo.org/id/dataset-parameter/1004091.rdf
Name: datastore_filetype
Units: unitless
Description: <p>Type of files available to download from SRA</p>
http://lod.bco-dmo.org/id/dataset-parameter/1004092.rdf
Name: datastore_provider
Units: unitless
Description: <p>Locations of where the files are available to download from</p>
http://lod.bco-dmo.org/id/dataset-parameter/1004093.rdf
Name: datastore_region
Units: unitless
Description: <p>Regions of where the data is located</p>
http://lod.bco-dmo.org/id/dataset-parameter/1004094.rdf
Name: experiment
Units: unitless
Description: <p>The accession in the form of SRX######## (ERX or DRX for INSDC partners)</p>
http://lod.bco-dmo.org/id/dataset-parameter/1004095.rdf
Name: genotyped_individual
Units: unitless
Description: <p>Simplified sample name that drops reef id from string</p>
http://lod.bco-dmo.org/id/dataset-parameter/1004096.rdf
Name: collection_date
Units: unitless
Description: <p>The collection date of the sample</p>
http://lod.bco-dmo.org/id/dataset-parameter/1004097.rdf
Name: geo_loc_name_country
Units: unitless
Description: <p>Name of the country where the sample was collected</p>
http://lod.bco-dmo.org/id/dataset-parameter/1004098.rdf
Name: geo_loc_name_country_continent
Units: unitless
Description: <p>Name of the continent where the sample was collected</p>
http://lod.bco-dmo.org/id/dataset-parameter/1004099.rdf
Name: geo_loc_name
Units: unitless
Description: <p>Full location of collection</p>
http://lod.bco-dmo.org/id/dataset-parameter/1004100.rdf
Name: latitude
Units: decimal degrees
Description: <p>Latitude where the sample was collected, North is positive</p>
http://lod.bco-dmo.org/id/dataset-parameter/1004102.rdf
Name: longitude
Units: decimal degrees
Description: <p>Longitude where the sample was collected, West is negative</p>
http://lod.bco-dmo.org/id/dataset-parameter/1004104.rdf
Name: isolate
Units: unitless
Description: <p>Denotes the experimental block (local geographical source) from which an individual oyster sample was taken.</p>
http://lod.bco-dmo.org/id/dataset-parameter/1004105.rdf
Name: isolation_source
Units: unitless
Description: <p>Denotes the reef ID within an experimental block (local geographical source) from which an individual oyster sample was taken.</p>
http://lod.bco-dmo.org/id/dataset-parameter/1004106.rdf
Name: instrument
Units: unitless
Description: <p>Name of the sequencing instrument model</p>
http://lod.bco-dmo.org/id/dataset-parameter/1004107.rdf
Name: libraryselection
Units: unitless
Description: <p>Library selection methodology (i.e. PCR, RANDOM, etc)</p>
http://lod.bco-dmo.org/id/dataset-parameter/1004108.rdf
Name: librarysource
Units: unitless
Description: <p>Source of the biological data (i.e. GENOMIC, METAGENOMIC, etc)</p>
http://lod.bco-dmo.org/id/dataset-parameter/1004109.rdf
Name: organism
Units: unitless
Description: <p>Scientific name of the organism that was sequenced (as found in the NCBI Taxonomy Browser)</p>
http://lod.bco-dmo.org/id/dataset-parameter/1004110.rdf
Name: platform
Units: unitless
Description: <p>Name of the sequencing platform (i.e. ILLUMINA)</p>
http://lod.bco-dmo.org/id/dataset-parameter/1004111.rdf
Name: releasedate
Units: unitless
Description: <p>The date on which the data was released</p>
http://lod.bco-dmo.org/id/dataset-parameter/1004112.rdf
Name: primary_genetic_assignment
Units: unitless
Description: <p>Assigned genetic cluster for an individual using the primary genetic assignment set applied to all main text analyses (DAPC approach, SNP set filtered for MAF > 0.01, LD pruning, and Fall 2020 missing data). Label names correspond to the state of origin of the hatchery source associated with a given genetic cluster (gME, gMA, gNY, gVA).</p>
http://lod.bco-dmo.org/id/dataset-parameter/1004113.rdf
Name: excluded_from_reeflevel_analyses
Units: unitless
Description: <p>Flag indicating whether an individual was excluded from reef-level analyses (i.e., if collected as initial source hatchery sample, extra reef samples from 2019 or 2021, or from reefs shown to have started as single source reefs in 2018). NA if sample not excluded.</p>
http://lod.bco-dmo.org/id/dataset-parameter/1004114.rdf
Name: Title
Units: unitless
Description: <p>Biosample title</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://osprey.bco-dmo.org/dataset/1003894/data/download
download
onLine
dataset
<p>These data were published in Truskey et al. 2025 (Evolutionary Applications). All figure numbers and supplementary materials mentioned refer to Truskey et al. 2025 (Evolutionary Applications).</p>
<p><strong>Restoration experiment and sample collection</strong></p>
<p>In April 2017, we collaborated with local oyster farmers to source oyster eyed-larvae from four commercial hatcheries for the construction of new experimental oyster reefs in Ninigret Pond (Charlestown, Rhode Island, USA). Hatchery sources were selected across a broad geographic sampling range to maximize diversity (Figure&nbsp;1a of Truskey et al. 2025). They included two regional hatcheries, one from Massachusetts (MA) and one from New York (NY), and two more distant hatcheries, one from Maine (ME) and one from Virginia (VA). A local Rhode Island hatchery facility received oyster eyed-larvae from each source hatchery, set the eyed-larvae on dead oyster and/or clam shell (hereafter referred to as spat-on-shell oysters), and distributed the spat-on-shell oysters to three local oyster growers (Grower 1: MA; Grower 2: ME, NY, VA; Grower 3: NY, VA) who maintained these juvenile oysters on separate leased oyster farm plots prior to reef construction. Immediately prior to reef construction, we collected 20 juvenile spat-on-shell oysters from each grower-hatchery source combination for genetic analysis (<em>n</em> = 6 combinations; Grower 1-MA; Grower 2-ME; Grower 2-NY; Grower 2-VA; Grower 3-NY; Grower 3-VA).</p>
<p>In October and November 2017, we constructed 16 subtidal reefs within a no-harvest Shellfish Management Area in Ninigret Pond. Reefs were created across four 0.025-acre experimental blocks, with four reefs per block (Figure&nbsp;2 of Truskey et al. 2025). Each reef consisted of a base layer of 0.25 cubic yards of dead oyster or clam shell deployed in October and topped with 1.25 cubic yards of spat-on-shell oysters in early November from the stock grown out by the local oyster growers. Our experiment was originally designed to seed three reefs per block with a different single hatchery source from the four available hatchery sources and to seed the fourth reef per block with a mixed combination of the three sources (e.g., Reef 1: ME, Reef 2: MA, Reef 3: NY, Reef 4: ME+MA+NY). However, analysis of the hatchery samples from oyster growers collected prior to reef construction revealed an early, unintended mixing of some of the sources (Appendix&nbsp;S1 of Truskey et al. 2025; Figure&nbsp;S1 of Truskey et al. 2025), resulting in mixtures of multiple sources on 12 out of the 16 constructed reefs. Thus, we focused our analyses on the actual genetic composition of each reef as determined by genetic sampling at two time points (fall 2018, fall 2020).&nbsp;</p>
<p>In fall 2018, we haphazardly sampled live oysters from each reef on scuba or snorkel (<em>N</em> = 512 individuals total, 32 per reef). Oysters were put on ice and transported to the Northeastern University Marine Science Center where they were held at −80°C until DNA extraction. By the fall of 2020, live oyster densities on all experimental reefs had declined, reflecting mortality of the original planted oysters and a lack of recruitment, consistent with other data from this system (Barrett et&nbsp;al.&nbsp;2024). To assess whether this mortality was associated with a consistent change in the genetic composition of surviving oysters on reefs, we repeated our sampling in fall 2020 and compared the resulting reef genetic profiles to those from fall 2018. Reef sample sizes varied at this time point due to low live abundances (<em>N</em> = 249 individuals total, ranging from 8 to 32 per reef).</p>
<p><strong>DNA extraction, RADseq library preparation, and bioinformatics</strong></p>
<p>Genomic DNA was extracted using the E-Z 96 Tissue DNA Kit (Omega-Biotek, Norcross, GA) following the animal tissue protocol with tissue centrifugation. Double-digest restriction-site-associated DNA (ddRAD) libraries with individually barcoded samples were prepared in three batches following Parchman et al. (2012): (1) initial hatchery samples (n = 120), (2) fall 2018 reef samples (n = 480; 30 oysters per reef across 16 reefs), and (3) fall 2020 reef samples (n = 248). For additional details on ddRAD library preparation, see Appendix S2 of Truskey et al. 2025. All libraries were sequenced with 100-bp single-end reads on an Illumina platform. The initial and fall 2020 batches were sequenced on a single lane of the Illumina HiSeq 2500 at Tufts University Core Facility Genomics; the fall 2018 batch was sequenced on two lanes of the Illumina NovaSeq 6000 at the University of Texas at Austin Genomic Sequencing and Analysis Facility.</p>
Specified by the Principal Investigator(s)
<p><strong>SNP calling, filtering, and defining datasets</strong></p>
<p>Raw sequence quality was assessed with FastQC v0.11.9 (Andrews 2010), and files were demultiplexed using the process_radtags function in STACKS v2.41 (Catchen et al. 2013). Read trimming, mapping, SNP calling, and genotyping were performed with the dDocent pipeline v2.9.4 (Puritz et al. 2014), with reads mapped to the <em>C. virginica</em> genome pruned for haplotigs (Puritz et al. 2024). Variant calling was performed using Freebayes v1.3.6 (Garrison and Marth 2012). SNP loci were then filtered using vcftools v0.1.16 (Danecek et al. 2011) following standard iterative quality filtering procedures for RADseq-generated SNP data (O'Leary et al. 2018), including filters for minor allele count, base quality, genotype call rate, and read depth, followed by individual-level filtering for missing data. Because genetic assignment approaches can be sensitive to the SNP dataset used, we generated 12 SNP sets varying in minor allele frequency (MAF) threshold, locus-level filtering for missingness specific to the fall 2020 library, and pruning for high linkage disequilibrium (LD), to evaluate the robustness of downstream genetic cluster assignments to these bioinformatic decisions. Filtering outcomes for each SNP set are detailed in Table S1 of Truskey et al. 2025.</p>
<p>The individuals presented in this dataset are all of those retained after SNP filtering steps and used in subsequent analyses to generate individual assignments to genetic clusters.</p>
Specified by the Principal Investigator(s)
- Loaded biosample_parsed.csv with missing values defined as empty string, "nd", and "NA"
- Loaded SraRunTable_updated_BCODMO_resubmission.csv as table "sra_run_metadata", with missing values defined as empty string, "nd", and "NA"
- Split the lat_lon column (e.g. "41.354865 N, -71.692945 W") into four intermediate columns: lat_value, lat_hemisphere, lon_value, lon_hemisphere, retaining the original lat_lon column
- Set lat_value and lon_value columns to number type temporarily to support downstream math computation
- Computed a new latitude column: negated lat_value when lat_hemisphere equaled "S", otherwise kept lat_value as-is
- Computed a new longitude column: negated lon_value when lon_hemisphere equaled "W", otherwise kept lon_value as-is
- Deleted the intermediate columns lat_lon, lat_value, lat_hemisphere, lon_value, lon_hemisphere, leaving only the new latitude and longitude columns
- Joined the biosample_parsed table into the sra_run_metadata table using a full-outer join, bringing in the SRS and Title columns (first-match aggregation), and deleted the biosample_parsed table afterward
- Output as 1003894_v1_oysters_sra_run_metadata.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 HiSeq 2500
Illumina HiSeq 2500
PI Supplied Instrument Name: Illumina HiSeq 2500 PI Supplied Instrument Description:The initial and fall 2020 batches were sequenced on a single lane of the Illumina HiSeq 2500 at Tufts University Core Facility Genomics; the fall 2018 batch was sequenced on two lanes of the Illumina NovaSeq 6000 at the University of Texas at Austin Genomic Sequencing and Analysis Facility. 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:The initial and fall 2020 batches were sequenced on a single lane of the Illumina HiSeq 2500 at Tufts University Core Facility Genomics; the fall 2018 batch was sequenced on two lanes of the Illumina NovaSeq 6000 at the University of Texas at Austin Genomic Sequencing and Analysis Facility. 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: PI Supplied Instrument Description:In fall 2018, we haphazardly sampled live oysters from each reef on scuba or snorkel (N = 512 individuals total, 32 per reef). Oysters were put on ice and transported to the Northeastern University Marine Science Center where they were held at −80°C until DNA extraction. 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 PI Supplied Instrument Description:In fall 2018, we haphazardly sampled live oysters from each reef on scuba or snorkel (N = 512 individuals total, 32 per reef). Oysters were put on ice and transported to the Northeastern University Marine Science Center where they were held at −80°C until DNA extraction. 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