Dataset: Juan de Fuca Viruses

Name: Collection information and genetic accession identifiers for Single Amplified Virus Genomes from hydrothermal fluids at IODP HOLE U1362B CORK observatory from R/V Atlantis cruise AT18-07 ROV Jason dives at the Juan de Fuca Ridge Flank in July of 2011
Published: 2022-05-23
Keywords: oceans

Cite This Dataset

DOI:10.26008/1912/bco-dmo.717763.2

Spatial Extent: N:47.75833 E:-127.76219 S:47.75833 W:-127.76219

Temporal Extent: 2016-03-11

Project:

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

Program:

Center for Dark Energy Biosphere Investigations (C-DEBI)

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)

Version:

Version Date:

2022-05-23

Restricted:

Release Date:

2018-09-30

Validated:

Yes

Current State:

Final no updates expected

Collection information and genetic accession identifiers for Single Amplified Virus Genomes from hydrothermal fluids at IODP HOLE U1362B CORK observatory from R/V Atlantis cruise AT18-07 ROV Jason dives at the Juan de Fuca Ridge Flank in July of 2011

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Archival Copy

Version Date	Archive	Persistent Identifier (PID)	Date PID Issued
2022-05-23	Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)	10.26008/1912/bco-dmo.717763.2	2022-05-24

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

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

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.

Data Files

File
viruses.csv (Comma Separated Values (.csv), 2.85 KB) MD5:6a47d8e601385f9fd9fa83e829e212d1 Primary data file for dataset ID 717763

More Information about this dataset

Funding Sources

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

Deployments

Deployment	Synonyms	Start Date	Platform	Investigator
AT18-07		2011-06-29	R/V Atlantis	Andrew Fisher (Chief Scientist)	data info

Instruments

None available yet

Parameters

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

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

Status message

Database

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Dataset: Juan de Fuca Viruses