Dataset: Quantitative PCR data
Deployment: Malaspina_2011

Quantitative PCR targeting Trichodesmium, UCYN-A, UCYN-B, gamma-24774A11, and Het1, based on the nifH gene.

Principal Investigator:

Pia Moisander (University of Massachusetts Dartmouth SMAST, UMASSD-SMAST)

Co-Principal Investigator:

Mar Benavides (Université de Toulon)

BCO-DMO Data Manager:

Hannah Ake (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Project:

Microbial associations in zooplankton: significance for the marine nitrogen cycle (Microbial associations in zooplankton)

Current State:

Final no updates expected

Version:

Final

Version Date:

2017-02-02

Data URL:

https://www.bco-dmo.org/dataset-deployment/680976/data

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Description

Quantitative PCR targeting Trichodesmium, UCYN-A, UCYN-B, gamma-24774A11, and Het1, based on the nifH gene.

Methods & Sampling

Dataset acquisition description

Samples were collected from Niskin bottles, filtered, and processed for DNA analyses. For detailed methods see Benavides et al. 2016.

Data Processing Description

Dataset Processing Description

For qPCR methods, see Benavides et al. 2016.

BCO-DMO Data Processing Notes:
-Reformatted column names to comply with BCO-DMO standards
-Added ISO_DateTime_UTC column
-Filled in blank cells with nd
-Reformatted date to YYYY/MM/DD

More information about this dataset deployment

Funding

Award Number	Funding Source
OCE-1130495	NSF Division of Ocean Sciences

Instruments

Thermal Cycler

Supplied Name: PCR

Supplied Description:

Used to process PCR samples

Instrument Type

Generic Name: Thermal Cycler

Generic Description:

A thermal cycler or "thermocycler" is a general term for a type of laboratory apparatus, commonly used for performing polymerase chain reaction (PCR), that is capable of repeatedly altering and maintaining specific temperatures for defined periods of time. The device has a thermal block with holes where tubes with the PCR reaction mixtures can be inserted. The cycler then raises and lowers the temperature of the block in discrete, pre-programmed steps. They can also be used to facilitate other temperature-sensitive reactions, including restriction enzyme digestion or rapid diagnostics.

(adapted from http://serc.carleton.edu/microbelife/research_methods/genomics/pcr.html)

Parameters

Supplied Name	Supplied description	Supplied Units	Standard Name
number	Sample ID number	unitless	sample
project	PI issued project name	unitless	project
date	Date of sampling; YYYY/mm/dd	unitless	date
time	Time of sampling; HH:MM	unitless	time
station	Station where sampling occurred	unitless	station
lat	Latitude; N is positive	decimal degrees	lat
lon	Longitude; E is positive	decimal degrees	lon
size_fraction	Filter size	microns	filter_size
UCYN_A	UCYN-A gene copy concentration	genes per liter	genetic_conc
Gamma_24774A11	Gamma 24774A11 gene copy concentration	genes per liter	genetic_conc
group_B	Group B gene copy concentration	genes per liter	genetic_conc
Tricho	Tricho gene copy concentration	genes per liter	genetic_conc
Het1	Het1 gene copy concentration	genes per liter	genetic_conc
ISO_DateTime_UTC	Date/Time (UTC) ISO formatted	unitless	ISO_DateTime_UTC

Database

Contribute Data

Dataset: Quantitative PCR data
Deployment: Malaspina_2011

Dataset acquisition description

Dataset Processing Description

Database

Contribute Data

Dataset: Quantitative PCR dataDeployment: Malaspina_2011

Dataset acquisition description

Dataset Processing Description

Dataset: Quantitative PCR data
Deployment: Malaspina_2011