Dataset: SMILE counts
Deployment: SKQ201703S

SMILE counts

Principal Investigator:

Anne Thompson (Portland State University, PSU)

BCO-DMO Data Manager:

Shannon Rauch (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Project:

Microbial ecology of coexisting ecotypes: Are all Prochlorococcus equal? (ProEco)

Deployment Synonyms:

SMILE

Data URL:

https://www.bco-dmo.org/dataset-deployment/736705/data

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Description

Counts of prochlorococcus, synechococcus, and picoeukaryotes from SMILE cruise (SKQ201703S) at the North Pacific Subtropical Front in March 2017.

Methods & Sampling

Dataset acquisition description

Water was sampled from the CTD into 15mL sterile polypropylene tubes. 2mL samples were fixed with 0.125% glutaraldehyde then flash frozen in liquid nitrogen and stored until analysis.

Cell counts were determined by flow cytometry using a BD Biosciences Influx high speed cell sorter. A 488nm laser was used in addition to chlorophyll and phycoerythrin filters, forward scatter relative to 1um beads, and side scattered light.

Data Processing Description

Dataset Processing Description

The program BD Software was using to collect flow cytometry data and generate distinct files for analysis. The program Flow Jo (version 7.6.5) was used to process flow cytometry files.

BCO-DMO Processing:
- modified parameter names to conform with BCO-DMO naming conventions;
- created date field with month and year (original dataset only had column for day of march);
- changed lon values from positive degrees west to negative degrees east.

More information about this dataset deployment

Funding

Award Number	Funding Source
OCE-1646709	NSF Division of Ocean Sciences

Instruments

CTD - profiler

Supplied Name:

Supplied Description:

Instrument Type

Generic Name: CTD - profiler

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

Generic Description:

The Conductivity, Temperature, Depth (CTD) unit is an integrated instrument package designed to measure the conductivity, temperature, and pressure (depth) of the water column. The instrument is lowered via cable through the water column. It permits scientists to observe the physical properties in real-time via a conducting cable, which is typically connected to a CTD to a deck unit and computer on a ship. The CTD is often configured with additional optional sensors including fluorometers, transmissometers and/or radiometers. It is often combined with a Rosette of water sampling bottles (e.g. Niskin, GO-FLO) for collecting discrete water samples during the cast.

This term applies to profiling CTDs. For fixed CTDs, see https://www.bco-dmo.org/instrument/869934.

Flow Cytometer

Supplied Name: BD Biosciences Influx high speed cell sorter

Supplied Description:

Instrument Type

Generic Name: Flow Cytometer

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/LAB37/

Generic Description:

Flow cytometers (FC or FCM) are automated instruments that quantitate properties of single cells, one cell at a time. They can measure cell size, cell granularity, the amounts of cell components such as total DNA, newly synthesized DNA, gene expression as the amount messenger RNA for a particular gene, amounts of specific surface receptors, amounts of intracellular proteins, or transient signalling events in living cells.
(from: http://www.bio.umass.edu/micro/immunology/facs542/facswhat.htm)

Parameters

Supplied Name	Supplied description	Supplied Units	Standard Name
castNum	Cast number	unitless	cast
date	Year, month, and day of sampling (formatted as yyyy-mm-dd)	unitless	date
day_of_March	Day of the month	unitless	day
depth	Sample depth	meters	depth
latitude	Latitude; positive values = North	decimal degress	lat
longitude	Longitude; negative values = West	decimal degress	lon
temperature	Temperature	degrees Celsius	temp
salinity	Salinity	psu	sal
oxygen	Oxygen	micromoles per kilogram (umol/kg)	O2
PAR	PAR	unknown	PAR
prochlorococcus_per_mL	Prochlorococcus counts per mL	cells per milliliter	coccus_p
synechococcus_per_mL	Synechococcus counts per mL	cells per milliliter	coccus_s
picoeukaryotes_per_mL	Picoeukaryote counts per mL	cells per milliliter	pico_euks

Database

Contribute Data

Dataset: SMILE counts
Deployment: SKQ201703S

Dataset acquisition description

Dataset Processing Description

Database

Contribute Data

Dataset: SMILE countsDeployment: SKQ201703S

Dataset acquisition description

Dataset Processing Description

Dataset: SMILE counts
Deployment: SKQ201703S