Dataset: ssDNA-dsDNA viromes
Deployment: 1311-SV

ssDNA-dsDNA viromes from the Great Lakes, off Bermuda and the South Pacific

Principal Investigator:

Matthew Sullivan (Ohio State University)

Co-Principal Investigator:

Maureen L. Coleman (University of Chicago)

BCO-DMO Data Manager:

Nancy Copley (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Project:

Ecological impacts and drivers of double-stranded DNA viral communities in the global oceans (GOV)

Version:

Data URL:

https://www.bco-dmo.org/dataset-deployment/737547/data

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Description

This dataset includes metadata and links to scripts and data for the analyses of double- and single-stranded DNA from viruses collected in the Great Lakes, off Bermuda (N. Atlantic) and off Peru (S. Pacific) used to provide first estimates of the natural abundance of ssDNA viruses.

These data were published in
Roux S, Solonenko NE, Dang VT, Poulos BT, Schwenck SM, Goldsmith DB, Coleman ML, Breitbart M, Sullivan MB. (2016) Towards quantitative viromics for both double-stranded and single-stranded DNA viruses. PeerJ 4:e2777 DOI: 10.7717/peerj.2777

Methods & Sampling

Dataset acquisition description

For full methodology, see Roux et al (2016).

Great Lakes methodology:
For each lake, 33 to 45L of water were 0.22 micron m-filtered and viruses were concentrated from the filtrate using iron chloride flocculation followed by storage at 4 degrees C. After resuspension in ascorbic-EDTA buffer (0.1 M EDTA, 0.2 M Mg, 0.2 M ascorbic acid, pH 6.0), viral particles were concentrated using Amicon Ultra 100 kDa centrifugal devices (Millipore), treated with DNase I (100U/mL) followed by the addition of 0.1 M EDTA and 0.1 M EGTA to halt enzyme activity, and extracted with the QIAamp DNA Mini Kit (Qiagen 51304).

Tara Expedition methodology:
20 L of seawater were 0.22 μ m-filtered, and viruses were concentrated from the filtrate using iron chloride flocculation followed by storage at 4°C. After resuspension in ascorbic-EDTA buffer (0.1 M EDTA, 0.2 M Mg, 0.2 M ascorbic acid, pH 6.0), viral particles were concentrated using Amicon Ultra 100 kDa centrifugal devices (Millipore), treated with DNase I (100U/mL) followed by the addition of 0.1 M EDTA and 0.1 M EGTA to halt enzyme activity, and extracted with the QIAamp DNA Mini Kit (Qiagen 51304).

Bermuda BATS methodology:
Approximately 180L of seawater were concentrated using a 100kDa tangential flow filter, 0.22 μ m-filtered, PEG precipitated, cesium chloride purified, and DNA was extracted using formamide.

Data Processing Description

Dataset Processing Description

Trimmed and filtered reads were assembled with Spades 3.6.2 with the "sc" and "careful" options. All contigs >500 bp and with at least one complete gene were run through VirSorter in the "virome decontamination" mode as well as a custom detection pipeline for small genomes (see Roux et al., 2016). Contig affiliation was based on best BLAST hit against RefSeqVirus (thresholds: bit score > 50 and e-value < 10 −3 ).

BCO-DMO Processing:
- created a table with dataset id, description, latitude, longitude, depth and link to the sequence and associated data at iVirus
- added conventional header with dataset name, PI name, version date

More information about this dataset deployment

Funding

Award Number	Funding Source
OCE-1536989	NSF Division of Ocean Sciences

Instruments

Automated DNA Sequencer

Supplied Name:

Supplied Description:

Instrument Type

Generic Name: Automated DNA Sequencer

Acronym: Automated Sequencer

Generic Description:

General term for a laboratory instrument used for deciphering the order of bases in a strand of DNA. Sanger sequencers detect fluorescence from different dyes that are used to identify the A, C, G, and T extension reactions. Contemporary or Pyrosequencer methods are based on detecting the activity of DNA polymerase (a DNA synthesizing enzyme) with another chemoluminescent enzyme. Essentially, the method allows sequencing of a single strand of DNA by synthesizing the complementary strand along it, one base pair at a time, and detecting which base was actually added at each step.

Centrifuge

Supplied Name: Amicon Ultra 100 kDa centrifugal devices (Millipore)

Supplied Description:

Used to concentrate viral particles

Instrument Type

Generic Name: Centrifuge

Generic Description:

A machine with a rapidly rotating container that applies centrifugal force to its contents, typically to separate fluids of different densities (e.g., cream from milk) or liquids from solids.

Parameters

Supplied Name	Supplied description	Supplied Units	Standard Name
sample_type	type of analysis performed on the samples	unitless	sample_type
iVirus_link	hypertext link to the CyVerse iVirus data archive	unitless	external_link
iVirus_url	url for link to the CyVerse iVirus data archive	unitless	external_link
dataset_id	identifier for dataset	unitless	dataset_id
location	description of sample collection location	unitless	no_bcodmo_term
lat	latitude; north is positive	decimal degrees	lat
lon	longitude; east is positive	decimal degrees	lon
depth	sample depth	meters	depth

Database

Contribute Data

Dataset: ssDNA-dsDNA viromes
Deployment: 1311-SV

Dataset acquisition description

Dataset Processing Description

Database

Contribute Data

Dataset: ssDNA-dsDNA viromesDeployment: 1311-SV

Dataset acquisition description

Dataset Processing Description

Dataset: ssDNA-dsDNA viromes
Deployment: 1311-SV