Dataset: Raw metagenome and metatranscriptome from an Fe mat at Loihi Seamount

Name: Sample accession numbers for raw metagenome and metatranscriptome Illumina HiSeq 2500 sequencing from an Fe mat sampled during cruise TN293 to Loihi Seamount, Hawaii on 03/25/2013
Published: 2017-11-20
Keywords: biota, oceans

Cite This Dataset

Spatial Extent: N:18.901418 E:-155.258191 S:18.901418 W:-155.258191

Temporal Extent: 2013-03-25

Project:

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

Principal Investigator:

Clara Chan (University of Delaware)

BCO-DMO Data Manager:

Shannon Rauch (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Version:

20 November 2017

Version Date:

2017-11-20

Restricted:

Validated:

Yes

Current State:

Final no updates expected

Sample accession numbers for raw metagenome and metatranscriptome Illumina HiSeq 2500 sequencing from an Fe mat sampled during cruise TN293 to Loihi Seamount, Hawaii on 03/25/2013

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Description

This dataset includes accession numbers and links to NCBI SRA for metagenomic and metatranscriptomic reads from BioProject PRJNA412510. Samples were collected during the R/V Thomas G. Thompson cruise TN293 at Loihi Seamount. A single Fe mat was sampled (J2-674-BM1-C123456) at Pohaku (Mkr #57), with syringe J2-674-BM1-C3 used for metagenomic sequencing and syringe J2-674-BM1-C6 used for metatranscriptomic sequencing. Latitude: 18.901418 N; Longitude: 155.258191 W; Depth: 1179.43 meters below sea level.

Further details on sequencing are available on the NCBI BioProject page.

Methods & Sampling

Microbial mat samples were 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 collected at the seafloor with RNALater within each collection syringe, fixing RNA activity on collection (in situ RNA expression profiles). On return to the ship, samples were allowed to settle, and the settled floc was stored at -80 degrees C until extraction and analysis.

Data Processing Description

DNA and RNA were extracted as described in Chan et al. (2018). Raw metagenomic sequences were quality controlled, assembled, and binned (metagenome-assembled genomes [MAGs]), after which quality controlled RNA sequences were recruited to MAGs to estimate gene expression.

Data Files

File
Fe_mat_accessions_Chan.csv (Comma Separated Values (.csv), 308 bytes) MD5:4b81965ae165b96ee8e06fffa641d5b9 Primary data file for dataset ID 719770

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-1155290

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:

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
lat	Latitude where sample was collected; N = positive.	decimal degrees	lat
lon	Longitude where samples were collected. E = positive.	decimal degrees	lon

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Database

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Dataset: Raw metagenome and metatranscriptome from an Fe mat at Loihi Seamount