Dataset: Kaneohe Bay RNA virus metagenomes
Deployment: KaneoheBay_Steward

Pyrosequencing reads (454) of marine RNA virus metagenomes

Principal Investigator:

Grieg Steward (University of Hawaiʻi at Mānoa, SOEST)

Co-Principal Investigator:

Dr Alexander Culley (University of Hawaiʻi at Mānoa, SOEST)

Dr Guylaine Poisson (University of Hawaiʻi at Mānoa, SOEST)

BCO-DMO Data Manager:

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

Project:

Diversity and ecology of marine RNA viruses (Diversity and ecology of marine RNA viruses)

Current State:

Final no updates expected

Version:

2016-01-26

Version Date:

2016-01-26

Data URL:

https://www.bco-dmo.org/dataset-deployment/636488/data

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Description

This datasest links to accessions at the iMicrobe data repository containing fasta formatted nucleic acid sequences. Samples are from Surface waters of Kaneohe Bay, a tropical embayment on eastern shore of Oahu, HI, 21° 25’ 46.80” N, 157° 47’ 31.51” W.

Sample Name: CAM_SMPL_000815 (collected Aug 1, 2009)
Link: http://data.imicrobe.us/sample/view/333

Sample Name: CAM_SMPL_000824 (collected Jun 3, 2010)
Link: http://data.imicrobe.us/sample/view/324

Related References:

Culley AI, JA Mueller, M Belcaid, EM Wood-Charlson, G Poisson, GF Steward (2104). The characterization of RNA viruses in tropical seawater using targeted PCR and metagenomics. mBio 5(3):e01210-14. doi:10.1128/mBio.01210-14.

Steward GF, AI Culley, JA Mueller, EM Wood-Charlson, M Belcaid, G Poisson (2013). Are we missing half the viruses in the sea? ISME Journal 7(3) 627-679.

Methods & Sampling

Dataset acquisition description

454 Pyrosequencing on the GS FLX Titanium platform (Roche Diagnostics Corporation) was used to generate the sequence data.

Data Processing Description

Dataset Processing Description

Sequences were processed though the quality control pipeline of the RAST metagenomics server (http://metagenomics.anl.gov/?page=Home) to remove short and low-quality reads as well as artificial replicates.

More information about this dataset deployment

Funding

Award Number	Funding Source
DBI-0424599	NSF Division of Biological Infrastructure
GBMF1799	Gordon and Betty Moore Foundation
NIH-P20GM103466	National Institutes of Health
NIH-P20GM103516	National Institutes of Health
OCE-0826650	NSF Division of Ocean Sciences

Instruments

Automated DNA Sequencer

Supplied Name:

Supplied Description:

GS FLX Titanium platform (Roche Diagnostics Corporation)

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.

Parameters

Supplied Name	Supplied description	Supplied Units	Standard Name
sample	sample description	unitless	sample
sample_type	analysis type	unitless	sample_type
date	collection date; local time	yyyy-mm-dd	date
lat	latitude; north is positive	decimal degrees	lat
lon	longitude; east is positive	decimal degrees	lon
temp	surface temperature	degrees Celsius	temp
iMicrobe_accession	iMicrobe accession number with link	unitless	accession_number

Database

Contribute Data

Dataset: Kaneohe Bay RNA virus metagenomes
Deployment: KaneoheBay_Steward

Dataset acquisition description

Dataset Processing Description

Database

Contribute Data

Dataset: Kaneohe Bay RNA virus metagenomesDeployment: KaneoheBay_Steward

Dataset acquisition description

Dataset Processing Description

Dataset: Kaneohe Bay RNA virus metagenomes
Deployment: KaneoheBay_Steward