Dataset: SRA_CH0112 metadata
Deployment: CH0112

Physical meta associated with marine metagenome samples collected along the New England Shelf, USA

Principal Investigator:

George McManus (University of Connecticut, UConn - Avery Point)

Co-Principal Investigator:

BCO-DMO Data Manager:

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

Project:

Diversity and dynamics of planktonic ciliates - what can next-generation sequencing technologies tell us? (CiliateSequencing)

Version Date:

2015-11-19

Data URL:

https://www.bco-dmo.org/dataset-deployment/626699/data

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Description

Physical data associated with samples from NCBI BioProject SRA######, PRJNA297691 (not yet public, 2015-11-18)

References:

Santoferrara L.F., Grattepanche J-D., Katz L.A., McManus G.B. (submitted) Patterns and processes in microbial biogeography: do molecules and morphologies give the same answers?

Grattepanche J-D., Santoferrara L.F., McManus G.B., Katz L.A. (submitted) Unexpected biodiversity of ciliates in marine samples.

Methods & Sampling

Dataset acquisition description

Seawater samples were screened through a 80 um mesh, then sequentially filtered through 10 um and 2 um polycarbonate filters; DNA was extracted from half-filters.

Data Processing Description

Dataset Processing Description

Data were processed in SeaBird Seasave software, version 7.21a using instrument configuration files provided by RV Hatteras ship operations. Raw hexadecimal data files were converted to base 10. Processed data were imported into Excel.

More information about this dataset deployment

Funding

Award Number	Funding Source
OCE-1130033	NSF Division of Ocean Sciences

Instruments

CTD Sea-Bird 9

Supplied Name:

Supplied Description:

Instrument Type

Generic Name: CTD Sea-Bird 9

Acronym: CTD SBE 9

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/130/

Generic Description:

The Sea-Bird SBE 9 is a type of CTD instrument package. The SBE 9 is the Underwater Unit and is most often combined with the SBE 11 Deck Unit (for real-time readout using conductive wire) when deployed from a research vessel. The combination of the SBE 9 and SBE 11 is called a SBE 911. The SBE 9 uses Sea-Bird's standard modular temperature and conductivity sensors (SBE 3 and SBE 4). The SBE 9 CTD can be configured with auxiliary sensors to measure other parameters including dissolved oxygen, pH, turbidity, fluorometer, altimeter, etc.). Note that in most cases, it is more accurate to specify SBE 911 than SBE 9 since it is likely a SBE 11 deck unit was used. more information from Sea-Bird Electronics

Parameters

Supplied Name	Supplied description	Supplied Units	Standard Name
cruise_id	cruise identification	unitless	cruise_id
geo_loc_name	The geolocation of the collection: Atlantic Ocean	unitless	site
isolation_source	Source of the sample: seawater	unitless	no_bcodmo_term
organism	In this case the organism is a sample of marine seawater	unitless	no_bcodmo_term
samp_collect_device	sample collection device	unitless	instrument
depth_w	depth of water at sampling site	meters	depth_w
date_collected	date sample was collected	dd-Mon-yyyy	date
lat	latitude; north is positive	decimal degrees	lat
lon	longitude; east is positive	decimal degrees	lon
sample_name	sample identification	unitless	sample
layer_sampled	layer of water sampled	unitless	no_bcodmo_term
depth	depth of sample	meters	depth
temp	temperature	degrees Celsius	temp
sal	salinity	PSU	sal
O2	dissolved oxygen	mg L-1	O2
fluor	chlorophyll fluorescence	arbitrary units	fluor

Database

Contribute Data

Dataset: SRA_CH0112 metadata
Deployment: CH0112

Dataset acquisition description

Dataset Processing Description

Database

Contribute Data

Dataset: SRA_CH0112 metadataDeployment: CH0112

Dataset acquisition description

Dataset Processing Description

Dataset: SRA_CH0112 metadata
Deployment: CH0112