Dataset: 16S rRNA gene sequences from iron mats

Name: 16S rRNA gene sequences accessions from iron mats sampled during the R/V Thomas G. Thompson cruise TN293 in the Loihi Seamount, Hawaii from March to April 2013 (Ecology of Vent Mats project)
Published: 2017-06-30
Keywords: oceans

Cite This Dataset

Spatial Extent: N:18.92 E:-155.27 S:18.92 W:-155.27

Project:

Ecology of microbial mats at seamount associated Fe-rich hydrothermal vent systems (Ecology of Vent Mats)

Principal Investigator:

David Emerson (Bigelow Laboratory for Ocean Sciences)

Contact:

David Emerson (Bigelow Laboratory for Ocean Sciences)

BCO-DMO Data Manager:

Amber D. York (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Version Date:

2017-06-30

Restricted:

Validated:

Yes

Current State:

Final with updates expected

16S rRNA gene sequences accessions from iron mats sampled during the R/V Thomas G. Thompson cruise TN293 in the Loihi Seamount, Hawaii from March to April 2013 (Ecology of Vent Mats project)

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Description

This dataset contains accession numbers and links to NCBI GenBank for 16S rRNA gene sequences from iron mats for BioProject PRJEB10821. Samples were collected during the R/V Thomas G. Thompson cruise TN293 and used the ROV Jason 2 (dives J2-671 - J2-677) at Loihi Seamount, summit area (1300m) to base (5000m), lat/lon (18.9200, -155.2700).

These accessions are also available at the European Nucleotide Archive under the sample accessions numbers ERS1089449–ERS1089534, study accession number PRJEB10821.

Methods & Sampling

Microbial mat samples acquired with sub-centimeter sampling resolution from the seafloor using a novel microbial mat sampling device (see Breier, et al. 2012. for details) operated by the ROV Jason 2. Microbial mat samples were frozen on board the ship and returned to the laboratory for DNA extraction and analysis. The V4-V5 region of the 16S rRNA gene was sequenced using pyrosequencing (titanium chemistry) as described in Scott et al. 2015.

Data Processing Description

Raw data was processed using mothur and oligotyping/minimum entropy decomposition.

Data Files

File
Fe_mat_accessions.csv (Comma Separated Values (.csv), 9.96 KB) MD5:284b818c43c6d487cbb53ff1c6b13f32 Primary data file for dataset ID 707550

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-1155754

Deployments

Deployment	Synonyms	Start Date	Platform	Investigator
TN293	Loihi 2013	2013-03-16	R/V Thomas G. Thompson	Craig L. Moyer (Chief Scientist)	data info

Instruments

ROV Jason

Supplied Name: ROV Jason 2

Supplied Description:

Dives J2-671 - J2-677

Instrument Type

Generic Name: ROV Jason

Generic Description:

The Remotely Operated Vehicle (ROV) Jason is operated by the Deep Submergence Laboratory (DSL) at Woods Hole Oceanographic Institution (WHOI). WHOI engineers and scientists designed and built the ROV Jason to give scientists access to the seafloor that didn't require them leaving the deck of the ship. Jason is a two-body ROV system. A 10-kilometer (6-mile) fiber-optic cable delivers electrical power and commands from the ship through Medea and down to Jason, which then returns data and live video imagery. Medea serves as a shock absorber, buffering Jason from the movements of the ship, while providing lighting and a bird’s eye view of the ROV during seafloor operations. During each dive (deployment of the ROV), Jason pilots and scientists work from a control room on the ship to monitor Jason’s instruments and video while maneuvering the vehicle and optionally performing a variety of sampling activities. Jason is equipped with sonar imagers, water samplers, video and still cameras, and lighting gear. Jason’s manipulator arms collect samples of rock, sediment, or marine life and place them in the vehicle’s basket or on "elevator" platforms that float heavier loads to the surface. More information is available from the operator site at URL. https://ndsf.whoi.edu/jason/

Parameters

Date and time formats are described in python strftime() syntax.

Supplied Name	Supplied description	Supplied Units	Standard Name
accession_id	Accession number at NCBI	unitless	accession_number
accession_link	Link to accession at NCBI	unitless	external_link

Status message

Database

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Dataset: 16S rRNA gene sequences from iron mats