Dataset: Juan de Fuca Viruses
Deployment: AT18-07

Single Amplified Virus Genome sequence accessions at NCBI

View Data: For data, See Dataset Metadata Page: https://osprey.bco-dmo.org/dataset/717763

Principal Investigator:

Joaquín Martínez Martínez (Bigelow Laboratory for Ocean Sciences)

Contact:

Joaquín Martínez Martínez (Bigelow Laboratory for Ocean Sciences)

BCO-DMO Data Manager:

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

Project:

Viral genetic richness and functions that shape the microbial community at the Juan de Fuca Ridge (Juan de Fuca Viruses)

Version:

Expand/Collapse All

Description

This dataset contains information related to Single Amplified Virus Genomes originated from hydrothermal fluids collected at a deep-sea subsurface observatory. The accession numbers included in the dataset correspond to genetic sequences at the National Center for Biotechnology Information (NCBI, https://www.ncbi.nlm.nih.gov/). Genetic accessions are available at NCBI under BioProject PRJNA398661.

The sampling location was the Integrated Ocean Drilling Program (IODP) Hole U1362B subseafloor borehole ("CORK") observatory located at the Juan de Fuca Ridge Flank (47.75833, -127.76219) at a depth of 2658 m (280 m below seafloor). The samples were collected during ROV Jason dives conducted from the R/V Atlantis cruise AT18-07 on July 8th, 2011.

Methods & Sampling

Dataset acquisition description

Sampling and Analytical Methodology:

Deep-sea hydrothermal fluid samples were collected from the IODP Hole U1362B CORK observatory using a custom syringe sampler fired in the 'shimmering' effluent of a free-flow chimney connected to the ball valve of the CORK well-head. Upon recovery, fluids for this project were fixed with a glycerol Tris-EDTA buffer for subsequent single virus sorting and genomic analysis. Single virus-like particles were sorted separately by fluorescence activated sorting. DNA was amplified by Multiple Displacement Amplification.

Data Processing Description

Dataset Processing Description

BCO-DMO Data Manager Processing Notes:
* added a conventional header with dataset name, PI name, version date
* modified parameter names to conform with BCO-DMO naming conventions
* Since data are now public at NCBI, added columns Sample_Name,BioSample,SRA,Organism and remove Submission identifier.
* Added columns Lat,Lon to data table from metadata information.

More information about this dataset deployment

Funding

Award Number	Funding Source
OCE-0939564	NSF Division of Ocean Sciences

Instruments

None available yet

Parameters

Supplied Name	Supplied description	Supplied Units	Standard Name
Species_Name	Species Name	unitless	sample_descrip
Sample_Name	Sample Name	unitless	sample
BioSample	NCBI BioSample accession	unitless	BioSample
SRA	NCBI Sequence Read Archive Sample accession	unitless	SRA_sample
NCBI_BioProject	NCBI BioProject accession	unitless	BioProject
Types_of_Sequences	Sequence type (e.g. dsDNA genome)	unitless	sample_descrip
Location_collected	Geolocation of collection	unitless	site
Lat	Latitute of collection	decimal degrees	lat
Lon	Longitude of collection	decimal degrees	lat
Date_Collected	Collection date in ISO 8601 format YYYY-MM-DD	unitless	date
Sequencing_method	Sequencing method	unitless	sample_descrip
Analysis_method	Analysis method	unitless	sample_descrip
Organism	Organism (e.g. viral metagenome)	unitless	sample_descrip
Description	Description	unitless	sample_descrip

Database

Contribute Data

Dataset: Juan de Fuca Viruses
Deployment: AT18-07

Dataset acquisition description

Dataset Processing Description

Database

Contribute Data

Dataset: Juan de Fuca VirusesDeployment: AT18-07

Dataset acquisition description

Dataset Processing Description

Dataset: Juan de Fuca Viruses
Deployment: AT18-07