http://lod.bco-dmo.org/id/dataset/1007825
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
2026-09-16
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Bacterial 16S rRNA barcodes associated with methane seep invertebrates collected off of the Aleutian Islands, Gulf of Alaska on R/V Atlantis cruise AT50-24 from May to June 2024
2026-09-15
publication
2026-09-15
revision
BCO-DMO Linked Data URI
2026-09-15
creation
http://lod.bco-dmo.org/id/dataset/1007825
Shana Goffredi
Occidental College
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: Goffredi, S. (2026) Bacterial 16S rRNA barcodes associated with methane seep invertebrates collected off of the Aleutian Islands, Gulf of Alaska on R/V Atlantis cruise AT50-24 from May to June 2024. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2026-09-15 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/1007825 [access date]
Methods and Sampling: <p><strong>Sampling</strong></p>
<p>Seep invertebrates were collected from the Sanak seep off of Alaska in June 2024 (53.74865 N/ −162.58970 W; 2,020 m) aboard the R/V Atlantis (expedition AT50-24) with HOV Alvin (operated by the Woods Hole Oceanographic Institution). Specimens for molecular analysis were preserved within 2 h of collection in ~90% ethanol and stored at 4 °C. Total genomic DNA was extracted from whole specimens preserved in ethanol using the Qiagen DNeasy kit (Qiagen, Valencia, CA) according to the manufacturer’s instructions.</p>
<p><strong>Data Collection Methods</strong></p>
<p>Total DNA extracted was quantified via a Qubit 3.0 fluorometer using the dsDNA BR Assay Kit (Thermo Fisher Scientific). The V4-V5 hypervariable region of the 16S rRNA gene was PCR amplified using bacterial primers [515F: GTGYCAGCMGCCGCGGTAA and 806R: GGACTACHVGGGTWTCTAAT] with Illumina adapters on the 5′ end (San Diego, CA). Each PCR product was secondarily barcoded with Illumina NexteraXT index v2 Primers that included unique 8-bp barcodes, with NEB Q5 Hot Start High-Fidelity Mix at an annealing temperature of 66 °C for 11 cycles. Barcoded products were purified using Millipore-Sigma (St. Louis, MO) MultiScreen Plate MSNU03010 with a vacuum manifold and quantified using the QuantIT PicoGreen dsDNA Assay Kit (ThermoFisher Scientific) on a BioRad CFX96 Touch Real-Time PCR Detection System. Barcoded samples were combined in approximately equimolar amounts, purified again with Promega’s Wizard SV Gel and PCR Clean-up System (#A9281), and quantified again using the QuBit system. This sample was submitted to Laragen, Inc. (Culver City, CA) for 2× 250 bp paired-end analysis on the Illumina MiSeq platform with 20% PhiX addition.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-2048481 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=2048481
onGoing
Shana Goffredi
Occidental College
323-259-1470
1600 Campus Road
Los Angeles
CA
90041-3314
USA
sgoffredi@oxy.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
ASV
SG_AD5272_A1_Aplacophoran_W10267_S178
SG_AD5272_PC6_aplacophoran_BW_S148
SG_AD5272_PC6_aplacophoran_S144
SG_AD5273_BB16_hydroids_W10302_S179
SG_AD5273_BB16_Polycirrinae_1_S175
SG_AD5273_BRock_zonathid_brown_S181
SG_AD5273_BRock_zonathid_orange_S180
SG_AD5274_BT2_octocoral_S143
SG_AD5274_S1_gammarid_amphipod_S182
SG_AD5275_S5_octocoral_S145
SG_AD5278_BT3_encrusting_sponge_S159
SG_AD5278_S1_pycnogonid_S161
SG_AD5279_S4_pycnogonid_S162
SG_AD5280_R3_encrusting_sponge_S160
SG_AD5280_S4_Sibglinum_troph_S177
SG_Sanak_caprellid_AD5280_A1_S164
SG_Sanak_hydroids_AD5273_BB16_S165
SG_Sanak_isopod_AD5277_BT2_S163
domain
phylum
class
order
family
genus
Illumina MiSeq platform
Qubit 3.0 fluorometer (Thermo Fisher Scientific), using dsDNA BR Assay Kit
HOV Alvin manipulator and/or suction sampler
BioRad CFX96 Touch Real-Time PCR Detection System
theme
None, User defined
sequence
animal group (category)
taxon
phylum
taxonomic class
order
family
genus
featureType
BCO-DMO Standard Parameters
Automated DNA Sequencer
Fluorometer
HOV Alvin
Thermal Cycler
instrument
BCO-DMO Standard Instruments
AT50-24
service
Deployment Activity
Gulf of Alaska
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: Redefining the footprint of deep ocean methane seepage for benthic ecosystems
https://osprey.bco-dmo.org/project/840220
Collaborative Research: Redefining the footprint of deep ocean methane seepage for benthic ecosystems
<p><em>NSF Award Abstract:</em><br />
This research examines the role of deep-sea organisms in determining the fate and footprint of methane, a potent greenhouse gas, on Pacific continental margins. The investigators are evaluating the deep ocean methanosphere defined by the microbial communities that consume methane and the animals that directly feed on or form symbioses with methane-consuming microbes. They are also investigating animal communities that gain energy indirectly from methane, as well as those that take advantage of carbonate rocks, the physical manifestation of methane consumption in seafloor sediments. The study of methane seeps in the deep waters of both Alaska (4400-5500 meters) and Southern California (450-1040 meters) is enabling comparisons of the methanosphere under different food-limitation and oxygen regimes. By applying diverse chemical, isotopic, microscopy, and genetic-based analyses to seep microbes and fauna, this study is advancing understanding of the contribution of methane to deep-sea biodiversity and ecosystem function, information that can inform management and conservation actions in US waters. In addition to training for graduate and undergraduate students at their home institutions, the investigators are collaborating with the Alaska Native Science and Engineering Program (ANSEP). They are recruiting Alaskan undergraduates to participate in the research, contributing to ANSEP's online resources that promote interaction between scientists and middle and high school students, and participating in ANSEP's annual residential Career Exploration in Marine Science programs to engage middle school students in learning about deep-sea ecosystems and the variety of career pathways available in marine related fields.</p>
<p>Microbial production and consumption of methane is dynamic and widespread along continental margins, and some animals within deep-sea methane seeps rely on the oxidation and sequestration of methane for nutrition. At the same time, understanding of methane-dependent processes and symbioses in the deep-sea environment is still rudimentary. The goals of this study are to 1) examine the diversity of animals involved in methane-based symbioses and heterotrophic consumption of methane-oxidizing microbes and how these symbioses extend the periphery of seeps, contributing to non-seep, continental slope food webs; and 2) determine whether carbonates on the seep periphery sustain active methanotrophic microbial assemblages, providing a localized food source or chemical fuel for thiotrophic symbioses, via anaerobic oxidation of methane, or free-living, sulfide-oxidizing bacteria consumed by animals. The investigators are addressing these goals by surveying, sampling, and characterizing microbes, water, sediments, carbonates and animals at a deep seep site on the Aleutian Margin and a shallow site off Southern California. Shipboard experiments and laboratory analyses are using molecular, isotopic, geochemical, and radiotracer tools to understand transfer of methane-sourced carbon from aerobic methanotrophs under multiple oxygen levels, pressures, and photosynthetic food inputs. This approach offers a wide lens by which to examine the methane seep footprint, allow reinterpretation of past observations, and identify new scientific areas for future study. Improved characterization of the deep continental margin methanosphere informs climate science, biodiversity conservation, and resource management.</p>
Methanosphere
largerWorkCitation
project
eng; USA
oceans
Gulf of Alaska
-162.5896946
-117.7817591
32.9044241
57.4556716
2023-07-18
2024-06-02
Gulf of Alaska and Southern California Bight
0
BCO-DMO catalogue of parameters from Bacterial 16S rRNA barcodes associated with methane seep invertebrates collected off of the Aleutian Islands, Gulf of Alaska on R/V Atlantis cruise AT50-24 from May to June 2024
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/1008219.rdf
Name: ASV
Units: unitless
Description: <p>Amplicon sequence variant identifier</p>
http://lod.bco-dmo.org/id/dataset-parameter/1008220.rdf
Name: SG_AD5272_A1_Aplacophoran_W10267_S178
Units: read counts
Description: <p>host animal identity</p>
http://lod.bco-dmo.org/id/dataset-parameter/1008221.rdf
Name: SG_AD5272_PC6_aplacophoran_BW_S148
Units: read counts
Description: <p>host animal identity</p>
http://lod.bco-dmo.org/id/dataset-parameter/1008222.rdf
Name: SG_AD5272_PC6_aplacophoran_S144
Units: read counts
Description: <p>host animal identity</p>
http://lod.bco-dmo.org/id/dataset-parameter/1008223.rdf
Name: SG_AD5273_BB16_hydroids_W10302_S179
Units: read counts
Description: <p>host animal identity</p>
http://lod.bco-dmo.org/id/dataset-parameter/1008224.rdf
Name: SG_AD5273_BB16_Polycirrinae_1_S175
Units: read counts
Description: <p>host animal identity</p>
http://lod.bco-dmo.org/id/dataset-parameter/1008225.rdf
Name: SG_AD5273_BRock_zonathid_brown_S181
Units: read counts
Description: <p>host animal identity</p>
http://lod.bco-dmo.org/id/dataset-parameter/1008226.rdf
Name: SG_AD5273_BRock_zonathid_orange_S180
Units: read counts
Description: <p>host animal identity</p>
http://lod.bco-dmo.org/id/dataset-parameter/1008227.rdf
Name: SG_AD5274_BT2_octocoral_S143
Units: read counts
Description: <p>host animal identity</p>
http://lod.bco-dmo.org/id/dataset-parameter/1008228.rdf
Name: SG_AD5274_S1_gammarid_amphipod_S182
Units: read counts
Description: <p>host animal identity</p>
http://lod.bco-dmo.org/id/dataset-parameter/1008229.rdf
Name: SG_AD5275_S5_octocoral_S145
Units: read counts
Description: <p>host animal identity</p>
http://lod.bco-dmo.org/id/dataset-parameter/1008230.rdf
Name: SG_AD5278_BT3_encrusting_sponge_S159
Units: read counts
Description: <p>host animal identity</p>
http://lod.bco-dmo.org/id/dataset-parameter/1008231.rdf
Name: SG_AD5278_S1_pycnogonid_S161
Units: read counts
Description: <p>host animal identity</p>
http://lod.bco-dmo.org/id/dataset-parameter/1008232.rdf
Name: SG_AD5279_S4_pycnogonid_S162
Units: read counts
Description: <p>host animal identity</p>
http://lod.bco-dmo.org/id/dataset-parameter/1008233.rdf
Name: SG_AD5280_R3_encrusting_sponge_S160
Units: read counts
Description: <p>host animal identity</p>
http://lod.bco-dmo.org/id/dataset-parameter/1008234.rdf
Name: SG_AD5280_S4_Sibglinum_troph_S177
Units: read counts
Description: <p>host animal identity</p>
http://lod.bco-dmo.org/id/dataset-parameter/1008235.rdf
Name: SG_Sanak_caprellid_AD5280_A1_S164
Units: read counts
Description: <p>host animal identity</p>
http://lod.bco-dmo.org/id/dataset-parameter/1008236.rdf
Name: SG_Sanak_hydroids_AD5273_BB16_S165
Units: read counts
Description: <p>host animal identity</p>
http://lod.bco-dmo.org/id/dataset-parameter/1008237.rdf
Name: SG_Sanak_isopod_AD5277_BT2_S163
Units: read counts
Description: <p>host animal identity</p>
http://lod.bco-dmo.org/id/dataset-parameter/1008238.rdf
Name: domain
Units: unitless
Description: <p>Taxonomic designation of the representative bacteria at the level of Domain</p>
http://lod.bco-dmo.org/id/dataset-parameter/1008239.rdf
Name: phylum
Units: unitless
Description: <p>Taxonomic designation of the representative bacteria at the level of Phylum</p>
http://lod.bco-dmo.org/id/dataset-parameter/1008240.rdf
Name: class
Units: unitless
Description: <p>Taxonomic designation of the representative bacteria at the level of Class</p>
http://lod.bco-dmo.org/id/dataset-parameter/1008241.rdf
Name: order
Units: unitless
Description: <p>Taxonomic designation of the representative bacteria at the level of Order</p>
http://lod.bco-dmo.org/id/dataset-parameter/1008242.rdf
Name: family
Units: unitless
Description: <p>Taxonomic designation of the representative bacteria at the level of Family</p>
http://lod.bco-dmo.org/id/dataset-parameter/1008243.rdf
Name: genus
Units: unitless
Description: <p>Taxonomic designation of the representative bacteria at the level of Genus, if known</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
450974
https://datadocs.bco-dmo.org/file/m71GDvNtkRE807/1007825_v1_at50_24_bacterial_16s_barcodes.csv
1007825_v1_at50_24_bacterial_16s_barcodes.csv
Primary data file for dataset ID 1007825, version 1
Bacterial barcodes per sample, by ASV, and a file of corresponding ASV sequences.
download
541968706
https://datadocs.bco-dmo.org/file/4WA41MYIRxxM0Y/1007825_v1_at50_24_fastq.zip
1007825_v1_at50_24_fastq.zip
This compressed folder contained the raw paired-end 16S rRNA amplicon (V4 region) sequencing reads generated on an Illumina MiSeq (2×250 bp), primer-trimmed, for sample SG-AD5194-CT2 (Terebellid host), comprising 127,646 read pairs (R1/R2).
download
1337556
https://datadocs.bco-dmo.org/file/WWxmY3mSxkz0ok/1007825_v1_at50_24_sra_2026_Bacterial_16S_barcodes_asvs.fasta
1007825_v1_at50_24_sra_2026_Bacterial_16S_barcodes_asvs.fasta
This FASTA file contains bacterial barcodes per sample, by ASV, and a file of corresponding ASV sequences.
download
4387
https://datadocs.bco-dmo.org/file/oA37Gx7Cr3mrR0/1007825_v1_at50_24_sra_2026_project_info.csv
1007825_v1_at50_24_sra_2026_project_info.csv
This file contains metadata for samples that have corresponding bacterial barcoding data, including general host identity, sample date and geolocation, as well as the sample method and DNA extraction kit.
Parameter details:
Parameter name (i.e., column name), Parameter description, parameter units
"sample_name", "Sample name", "unitless"
"host", "animal host identity", "unitless"
"isolation_source", "isolation source", "unitless"
"collection_date", "Date of sample collection", "unitless"
"geo_loc_name", "geolocation", "unitless"
"lat", "latitude", "decimal degrees"
"lon", "longitude", "decimal degrees"
"samp_collect_device", "sample collection device", "unitless"
"samp_mat_process", "DNA extraction kit", "unitless"
"description", "description", "unitless"
"sample_type", "sample type", "unitless"
download
https://osprey.bco-dmo.org/dataset/1007825/data/download
download
onLine
dataset
<p><strong>Sampling</strong></p>
<p>Seep invertebrates were collected from the Sanak seep off of Alaska in June 2024 (53.74865 N/ −162.58970 W; 2,020 m) aboard the R/V Atlantis (expedition AT50-24) with HOV Alvin (operated by the Woods Hole Oceanographic Institution). Specimens for molecular analysis were preserved within 2 h of collection in ~90% ethanol and stored at 4 °C. Total genomic DNA was extracted from whole specimens preserved in ethanol using the Qiagen DNeasy kit (Qiagen, Valencia, CA) according to the manufacturer’s instructions.</p>
<p><strong>Data Collection Methods</strong></p>
<p>Total DNA extracted was quantified via a Qubit 3.0 fluorometer using the dsDNA BR Assay Kit (Thermo Fisher Scientific). The V4-V5 hypervariable region of the 16S rRNA gene was PCR amplified using bacterial primers [515F: GTGYCAGCMGCCGCGGTAA and 806R: GGACTACHVGGGTWTCTAAT] with Illumina adapters on the 5′ end (San Diego, CA). Each PCR product was secondarily barcoded with Illumina NexteraXT index v2 Primers that included unique 8-bp barcodes, with NEB Q5 Hot Start High-Fidelity Mix at an annealing temperature of 66 °C for 11 cycles. Barcoded products were purified using Millipore-Sigma (St. Louis, MO) MultiScreen Plate MSNU03010 with a vacuum manifold and quantified using the QuantIT PicoGreen dsDNA Assay Kit (ThermoFisher Scientific) on a BioRad CFX96 Touch Real-Time PCR Detection System. Barcoded samples were combined in approximately equimolar amounts, purified again with Promega’s Wizard SV Gel and PCR Clean-up System (#A9281), and quantified again using the QuBit system. This sample was submitted to Laragen, Inc. (Culver City, CA) for 2× 250 bp paired-end analysis on the Illumina MiSeq platform with 20% PhiX addition.</p>
Specified by the Principal Investigator(s)
<p>Raw reads were processed as follows: CutAdapt v4.1 was used to remove the primer sequences, which allowed one error for every 10 bp in the primer sequence. FastQC v1.13 was used to quality control the raw sequence data and identify trim cutoffs for both the forward and reverse reads, ahead of pairing. Raw sequences were then processed with DADA2 [for initial quality trimming, error rate estimation, merging of read pairs, chimeric sequence removal and community data matrix construction] and taxonomy was assigned to the processed ASVs (ASVs at 100% identity) using the SILVA database v138.1.</p>
Specified by the Principal Investigator(s)
Curation Actions Performed on Data
- Imported AT50-24_Bacterial 16S barcodes.xlsx from the first worksheet, using the first row as column headers. Floating-point errors were corrected, and the original cell formatting was preserved.
- Treated empty cells, nd, and NA as missing values.
- Named the resulting table 1007825_v1_alaskan_methane_seep_bacteria_16s_rrna_barcodes.
- Set the taxonomic columns (ASV, class, domain, family, genus, order, and phylum) as text fields.
- Set all sample barcode count columns as integer fields.
- Saved the processed data as 1007825_v1_alaskan_methane_seep_bacteria_16s_rrna_barcodes.csv.
- Sample names, and environmental metadata can be found within the supplemental file (1007825_v1_at50_24_sra_2026_project_info.csv).
Curation Actions Performed on Metadata
- The temporal range noted for this dataset relates to the sample collection periods represented in supplemental file 1007825_v1_at50_24_sra_2026_project_info.csv.
- All raw fastq files associated with this dataset are available in the supplemental files section within the compressed folder named 1007825_v1_at50_24_fastq.zip.
- The raw fasta file associated with the barcodes of this dataset are available in the supplemental file 1007825_v1_at50_24_sra_2026_Bacterial_16S_barcodes_asvs.fasta.
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 platform
Illumina MiSeq platform
PI Supplied Instrument Name: Illumina MiSeq platform PI Supplied Instrument Description:This sample was submitted to Laragen, Inc. (Culver City, CA) for 2× 250 bp paired-end analysis on the Illumina MiSeq platform with 20% PhiX addition. 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.
Qubit 3.0 fluorometer (Thermo Fisher Scientific), using dsDNA BR Assay Kit
Qubit 3.0 fluorometer (Thermo Fisher Scientific), using dsDNA BR Assay Kit
PI Supplied Instrument Name: Qubit 3.0 fluorometer (Thermo Fisher Scientific), using dsDNA BR Assay Kit PI Supplied Instrument Description:Total DNA extracted was quantified via a Qubit 3.0 fluorometer using the dsDNA BR Assay Kit (Thermo Fisher Scientific). Instrument Name: Fluorometer Instrument Short Name:Fluorometer Instrument Description: A fluorometer or fluorimeter is a device used to measure parameters of fluorescence: its intensity and wavelength distribution of emission spectrum after excitation by a certain spectrum of light. The instrument is designed to measure the amount of stimulated electromagnetic radiation produced by pulses of electromagnetic radiation emitted into a water sample or in situ. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/113/
HOV Alvin manipulator and/or suction sampler
HOV Alvin manipulator and/or suction sampler
PI Supplied Instrument Name: HOV Alvin manipulator and/or suction sampler PI Supplied Instrument Description:Seep invertebrates were collected from the Sanak seep off of Alaska in June 2024 (53.74865 N/ −162.58970 W; 2,020 m) aboard the R/V Atlantis (expedition AT50-24) with HOV Alvin (operated by the Woods Hole Oceanographic Institution). Instrument Name: HOV Alvin Instrument Short Name: Instrument Description: Human Occupied Vehicle (HOV) Alvin is part of the National Deep Submergence Facility (NDSF). Alvin enables in-situ data collection and observation by two scientists to depths reaching 6,500 meters, during dives lasting up to ten hours.
Commissioned in 1964 as one of the world’s first deep-ocean submersibles, Alvin has remained state-of-the-art as a result of numerous overhauls and upgrades made over its lifetime. The most recent upgrades, begun in 2011 and completed in 2021, saw the installation of a new, larger personnel sphere with a more ergonomic interior; improved visibility and overlapping fields of view; longer bottoms times; new lighting and high-definition imaging systems; improved sensors, data acquisition and download speed. It also doubled the science basket payload, and improved the command-and-control system allowing greater speed, range and maneuverability.
With seven reversible thrusters, it can hover in the water, maneuver over rugged topography, or rest on the sea floor. It can collect data throughout the water column, produce a variety of maps and perform photographic surveys. Alvin also has two robotic arms that can manipulate instruments, obtain samples, and its basket can be reconfigured daily based on the needs of the upcoming dive.
Alvin's depth rating of 6,500m gives researchers in-person access to 99% of the ocean floor. Alvin is a proven and reliable platform capable of diving for up to 30 days in a row before requiring a single scheduled maintenance day. Recent collaborations with autonomous vehicles such as Sentry have proven extremely beneficial, allowing PIs to visit promising sites to collect samples and data in person within hours of their being discovered, and UNOLs driven technological advances have improved the ability for scientific outreach and collaboration via telepresence
Alvin is named for Allyn Vine, a WHOI engineer and geophysicist who helped pioneer deep submergence research and technology.
(from https://www.whoi.edu/what-we-do/explore/underwater-vehicles/hov-alvin/, accessed 2022-09-09)
BioRad CFX96 Touch Real-Time PCR Detection System
BioRad CFX96 Touch Real-Time PCR Detection System
PI Supplied Instrument Name: BioRad CFX96 Touch Real-Time PCR Detection System PI Supplied Instrument Description:Total DNA extracted was quantified via a Qubit 3.0 fluorometer using the dsDNA BR Assay Kit (Thermo Fisher Scientific). 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)
Cruise: AT50-24
AT50-24
R/V Atlantis
Community Standard Description
International Council for the Exploration of the Sea
R/V Atlantis
vessel
AT50-24
Lisa A. Levin
University of California-San Diego Scripps
R/V Atlantis
Community Standard Description
International Council for the Exploration of the Sea
R/V Atlantis
vessel