Dataset: Ulleung Basin Phylochip

Name: Presence/absence of taxa detected with the Phylochip in a sediment core collected in the Ulleng Basin in 2011
Published: 2018-06-14
Keywords: oceans

Cite This Dataset

DOI:10.26008/1912/bco-dmo.746718.1

Spatial Extent: N:37 E:131 S:37 W:131

Temporal Extent: 2011 - 2011

Project:

The Effect of Methane on Microbial Community Distributions in the Ulleung Basin (Methane_Microbes)

Program:

Center for Dark Energy Biosphere Investigations (C-DEBI)

Principal Investigator:

Brandon Briggs (Oregon State University, OSU)

Co-Principal Investigator:

Frederick Colwell (Oregon State University, OSU)

BCO-DMO Data Manager:

Mathew Biddle (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Version:

Version Date:

2018-06-14

Restricted:

Validated:

Yes

Current State:

Final no updates expected

Presence/absence of taxa detected with the Phylochip in a sediment core collected in the Ulleng Basin in 2011

Abstract:

Presence/absence of taxa detected with the Phylochip in a sediment core collected in the Ulleng Basin in 2011.

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Archival Copy

Version Date	Archive	Persistent Identifier (PID)	Date PID Issued
2018-06-14	Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)	10.26008/1912/bco-dmo.746718.1	2021-05-20

Description

Presence/ absence of taxa detected with the Phylochip.

Methods & Sampling

In summary, sediment cores were collected using a Furor Hydraulic Piston Corer following the Integrated Ocean Drilling Program (IODP) guidelines for obtaining high quality microbiology cores. Aboard ship, whole round cores were subcored by paring the outer two cm of sediment with an alcohol and flame sterilized chisel. The sub-cores were placed into sterile Whirl Pak Bags and stored at -80C. DNA was extracted from 10g of sediment using a PowerMax Soil DNA extraction kit. DNA was amplified using 27F and 1492R (bacterial) or 4F and 1492R (archaeal) universal primers. 150ng of bacterial and 50ng of archaeal amplicons were hybridized to the PhyloChip array.

Data Processing Description

Data processing can be found in Briggs et al. (2013).

BCO-DMO Processing:

added conventional header with dataset name, PI name, version date
modified parameter names to conform with BCO-DMO naming conventions
adjusted the duplicate column header HY03682 to HY03682_A
appended latitude and longitude fields for mapping.

Data Files

File
Ulleung_Basin_PhyloChip.csv (Comma Separated Values (.csv), 157.47 KB) MD5:edd56b4270e66a088f71dbdd39cc2755 Primary data file for dataset ID 746718

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
Ulleung_Basin_Core		2011-01-01	Unknown Platform	Brandon Briggs (Principal Investigator)	data info

Instruments

Piston Corer

Supplied Name: Furor Hydraulic Piston Corer

Supplied Description:

Sediment cores were collected using a Furor Hydraulic Piston Corer following the Integrated Ocean Drilling Program (IODP) guidelines for obtaining high quality microbiology cores.

Instrument Type

Generic Name: Piston Corer

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/51/

Generic Description:

The piston corer is a type of bottom sediment sampling device. A long, heavy tube is plunged into the seafloor to extract samples of mud sediment. A piston corer uses a "free fall" of the coring rig to achieve a greater initial force on impact than gravity coring. A sliding piston inside the core barrel reduces inside wall friction with the sediment and helps to evacuate displaced water from the top of the corer. A piston corer is capable of extracting core samples up to 90 feet in length.

Parameters

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

Supplied Name	Supplied description	Supplied Units	Standard Name
Domain	Domain level phylogenetic classification	unitless	kingdom
Phylum	Phylum level phylogenetic classification	unitless	phylum
Subphylum	Subphylum level phylogenetic classification	unitless	phylum
Class	Class level phylogenetic classification	unitless	class
Order	Order level phylogenetic classification	unitless	order
Family	Familty level phylgenetic classification	unitless	family
BSR03691	Presence (1) Absence (0) in sample BSR03691	unitless	flag
BSR03692	Presence (1) Absence (0) in sample BSR03692	unitless	flag
BSR36165_A	Presence (1) Absence (0) in sample BSR36165_A	unitless	flag
HY03682	Presence (1) Absence (0) in sample HY03682	unitless	flag
HY03684	Presence (1) Absence (0) in sample HY03684	unitless	flag
HY03685	Presence (1) Absence (0) in sample HY03685	unitless	flag
HY03687	Presence (1) Absence (0) in sample HY03687	unitless	flag
HY03689	Presence (1) Absence (0) in sample HY03689	unitless	flag
HY03690	Presence (1) Absence (0) in sample HY03690	unitless	flag
HY03672	Presence (1) Absence (0) in sample HY03672	unitless	flag
HY03673	Presence (1) Absence (0) in sample HY03673	unitless	flag
HY03675	Presence (1) Absence (0) in sample HY03675	unitless	flag
HY03676	Presence (1) Absence (0) in sample HY03676	unitless	flag
HY03682_A	Presence (1) Absence (0) in sample HY03682_A	unitless	flag
HY36145_A	Presence (1) Absence (0) in sample HY36145_A	unitless	flag
HY36146_A	Presence (1) Absence (0) in sample HY36146_A	unitless	flag
HY36147_A	Presence (1) Absence (0) in sample HY36147_A	unitless	flag
HY36148_A	Presence (1) Absence (0) in sample HY36148_A	unitless	flag
HY36149	Presence (1) Absence (0) in sample HY36149	unitless	flag
HY36150_A	Presence (1) Absence (0) in sample HY36150_A	unitless	flag
HY36153_A	Presence (1) Absence (0) in sample HY36153_A	unitless	flag
HY36154_A	Presence (1) Absence (0) in sample HY36154_A	unitless	flag
HY36151_A	Presence (1) Absence (0) in sample HY36151_A	unitless	flag
HY36152_A	Presence (1) Absence (0) in sample HY36152_A	unitless	flag
SMI03648	Presence (1) Absence (0) in sample SMI03648	unitless	flag
SMI36123_A	Presence (1) Absence (0) in sample SMI36123_A	unitless	flag
SMI36124_A	Presence (1) Absence (0) in sample SMI36124_A	unitless	flag
SMI03647	Presence (1) Absence (0) in sample SMI03647	unitless	flag
SMI36126_A	Presence (1) Absence (0) in sample SMI36126_A	unitless	flag
SMI36127_A	Presence (1) Absence (0) in sample SMI36127_A	unitless	flag
SMI36128_A	Presence (1) Absence (0) in sample SMI36128_A	unitless	flag
SMI03649	Presence (1) Absence (0) in sample SMI03649	unitless	flag
SMI03650	Presence (1) Absence (0) in sample SMI03650	unitless	flag
lon	Longitude in decimal degrees east.	decimal degrees	lon
lat	Latitude in decimal degrees north.	decimal degrees	lat

Status message

Database

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Dataset: Ulleung Basin Phylochip