Dataset: Seep Sediment Metagenome ANM1 - Genbank BioSample SAMN00215736

Name: Seep sediment metagenome ANM1 from the R/V Atlantis AT15-53 cruise in the Santa Monica Basin during 2009 (Viruses in Methanotrophic Marine Ecosystems project)
Published: 2016-01-19
Keywords: oceans

Cite This Dataset

Spatial Extent: N:33.75 E:-118.67 S:33.75 W:-118.67

Project:

Dimensions: The Role of Viruses in Structuring Biodiversity in Methanotrophic Marine Ecosystems (Viruses in Methanotrophic Marine Ecosystems)

Program:

Dimensions of Biodiversity (Dimensions of Biodiversity)

Principal Investigator:

David L. Valentine (University of California-Santa Barbara, UCSB)

Contact:

David L. Valentine (University of California-Santa Barbara, UCSB)

BCO-DMO Data Manager:

Stephen R. Gegg (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Version:

19 January 2016

Version Date:

2016-01-19

Restricted:

Current State:

Final no updates expected

Seep sediment metagenome ANM1 from the R/V Atlantis AT15-53 cruise in the Santa Monica Basin during 2009 (Viruses in Methanotrophic Marine Ecosystems project)

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Description

Metagenomic sequence reads representing viruses from marine sediments at a methane seep — part of the Gordon and Betty Moore Marine Phage Metagenome Initiative

Location:
Pacific Ocean: Santa Monica Basin, offshore California; Depth 820m; Lat. 33.799N, Long. 118.646W

Related files and references:
Henn, M. R., Sullivan, M. B., Stange-Thomann, N., Osburne, M. S., Berlin, A. M., Kelly, L., … Chisholm, S. W. (2010). Analysis of High-Throughput Sequencing and Annotation Strategies for Phage Genomes. PLoS ONE, 5(2), e9083. doi:10.1371/journal.pone.0009083

Paul, B. G., Bagby, S. C., Czornyj, E., Arambula, D., Handa, S., Sczyrba, A., … Valentine, D. L. (2015). Targeted diversity generation by intraterrestrial archaea and archaeal viruses. Nature Communications, 6(1). doi:10.1038/ncomms7585

Methods & Sampling

Sampling and Analytical Methodology:
Metagenomic sequencing was performed at the Broad Institute on 454-FLX plates, as part of the Gordon and Betty Moore Marine Phage Metagenome Initiative (Henn et al. 2010). Detailed methods on processing of metagenomic sequences, assembly, and genome annotation are described in Paul et al. (2015).

Data Processing Description

Data Processing:
Sediment metagenome ANM1 consists of raw reads from 454-FLX sequencing. To procure the ANMV-1 genome, metagenomic reads were first preprocessed, then assembled as described in Paul et al. (2015).

Data Files

File
ANM1.csv (Comma Separated Values (.csv), 427 bytes) MD5:671ba9d1e77699634ef9c129f2c6b090 Primary data file for dataset ID 633015

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-1046144

Deployments

Deployment	Synonyms	Start Date	Platform	Investigator
AT15-53	SEEPS09	2009-09-13	R/V Atlantis	David L. Valentine (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
CruiseId	Official UNOLS Cruise Id	text	cruise_id
Site	Site Id	text	site
Site_Description	Site Description	text	site_descrip
Collection_Date	Collection Date	DD-Mon-YYYY	date
Latitude	Latitude (South is negative)	decimal degrees	lat
Longitude	Longitude (West is negative)	decimal degrees	lon
Depth	Depth	meters	depth
Description	Sample Description	text	sample_descrip
Accession	Accession Id	text	accession_number
Submission	Submission Id	text	dataset_id
Link	Link to Accession in Genbank	text	external_link

Status message

Database

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Dataset: Seep Sediment Metagenome ANM1 - Genbank BioSample SAMN00215736