Dataset: Kaneohe Bay RNA virus metagenomes

Name: Pyrosequencing reads (454) of marine RNA virus metagenomes collected Kaneohe Bay, HI during 2009 (Diversity and ecology of marine RNA viruses project)
Published: 2016-01-26
Keywords: biota, oceans

Cite This Dataset

Spatial Extent: N:21.436536 E:-157.777361 S:21.436536 W:-157.777361

Project:

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

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)

Version:

2016-01-26

Version Date:

2016-01-26

Validated:

Yes

Current State:

Final no updates expected

Pyrosequencing reads (454) of marine RNA virus metagenomes collected Kaneohe Bay, HI during 2009 (Diversity and ecology of marine RNA viruses project)

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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

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

Data 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.

Data Files

File
virus_metagenome.csv (Comma Separated Values (.csv), 384 bytes) MD5:a6b7378f5e435b3b3b87252b1e046354 Primary data file for dataset ID 636479

More Information about this dataset

Funding Sources

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

Deployments

Deployment	Synonyms	Start Date	Platform	Investigator
KaneoheBay_Steward		2009-08-01	lab UHawaii_SOEST	Grieg Steward (Principal Investigator)	data info

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:

A DNA sequencer is an instrument that determines the order of deoxynucleotides in deoxyribonucleic acid sequences.

Parameters

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

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

Status message

Database

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Dataset: Kaneohe Bay RNA virus metagenomes