Dataset: qPCR data from the Cariaco Meta-Omics Cruises
Deployment: CAR212_2

qPCR data from the CAR212 and CAR216 cruises.

Principal Investigator:

Virginia P. Edgcomb (Woods Hole Oceanographic Institution, WHOI)

Gordon T. Taylor (Stony Brook University - SoMAS, SUNY-SB SoMAS)

Co-Principal Investigator:

Dr Craig Taylor (Woods Hole Oceanographic Institution, WHOI)

BCO-DMO Data Manager:

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

Project:

Genetic and Metabolic Signatures of Marine Microorganisms in Oxygen Depleted and Varying Geochemical Seascapes (CariacoMetaOmics)

Current State:

Final with updates expected

Version:

final

Version Date:

2016-07-22

Data URL:

https://osprey.bco-dmo.org/dataset-deployment/652503/data

Expand/Collapse All

Description

Quantitative polymerase chain reaction (qPCR) data collected from molecular samples on the CAR212 and CAR216 cruises.

Methods & Sampling

Dataset acquisition description

All samples were collected via Niskin bottles.

DNA samples for qPCR were size fractionated into a >2.7um fraction and 0.2-2.7um fraction using a glass fiber filter pre filter in-line with a sterivex filter. DNA was preserved in lysis buffer, stored frozen, and transported back to the home laboratory. After thawing, DNA was extracted according to Frias-Lopez et al. 2008, modified by Ganesh et al. 2014. All qPCR assays were performed on an Mx3000P thermal cycler (Agilent) using the SYBRgreen filter. Assays were designed for the following genes according to the following references:

qPCR

Data Processing Description

Dataset Processing Description

All data were normalized to volume of seawater.

DMO Notes:

-transferred each qPCR data section into separate a data object.
-reformatted the date to comply with BCO-DMO standards.
-reformatted some column names to comply with BCO-DMO standards.

More information about this dataset deployment

Funding

Award Number	Funding Source
OCE-1335436	NSF Division of Ocean Sciences
OCE-1336082	NSF Division of Ocean Sciences

Instruments

Niskin bottle

Supplied Description:

All samples were collected via Niskin bottles.

Instrument Type

Generic Name: Niskin bottle

Community Identifier: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0412/

Generic Description:

A Niskin bottle (a next generation water sampler based on the Nansen bottle) is a cylindrical, non-metallic water collection device with stoppers at both ends. The bottles can be attached individually on a hydrowire or deployed in 12, 24, or 36 bottle Rosette systems mounted on a frame and combined with a CTD. Niskin bottles are used to collect discrete water samples for a range of measurements including pigments, nutrients, plankton, etc.

Thermal Cycler

Supplied Name: Mx3000P thermal cycler (Agilent)

Supplied Description:

All qPCR assays were performed on this thermal cycler using the SYBRgreen filter.

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
cruise_id	cariaco cruise number and leg number	unitless	cruise_id
date_start	start date; mm/dd/yyyy	unitless	date_start
depth	depth	meters	depth
bac16S_dna	copies of the bacterial 16S gene	x10^8/L	abundance
bac16S_dna_sd	standard deviation of the copies of the bacterial 16S gene	x10^8/L	std_dev
bac16S_dna_particulate	fraction of bacterial 16S genes in the greater than 2.7 um fraction	dimensionless	no_bcodmo_term
bac16S_dna_particulate_sd	standard deviation of the fraction of bacterial 16S genes in the greater than 2.7 um fraction	dimensionless	std_dev
arch16S_dna	copies of the archaeal 16S gene	x10^8/L	abundance
arch16S_dna_sd	standard deviation of the copies of the archaeal 16S gene	x10^8/L	std_dev
arch16S_dna_particulate	fraction of archaeal 16S genes in the greater than 2.7 um fraction	dimensionless	no_bcodmo_term
arch16S_dna_particulate_sd	standard deviation of the fraction of archaeal 16S genes in the greater than 2.7 um fraction	dimensionless	std_dev
sqrG1_dna	copies of the sqrG1 gene	x10^4/L	abundance
sqrG1_dna_sd	standard deviation of the copies of the sqrG1 gene	x10^4/L	std_dev
sqrG1_dna_particulate	fraction of sqrG1 genes in the greater than 2.7 um fraction	dimensionless	no_bcodmo_term
sqrG1_dna_particulate_sd	standard deviation of the fraction of sqrG1 genes in the greater than 2.7 um fraction	dimensionless	std_dev
sqrG4_dna	copies of the sqrG4 gene	x10^4/L	abundance
sqrG4_dna_sd	standard deviation of the copies of the sqrG4 gene	x10^4/L	std_dev
sqrG4_dna_particulate	fraction of sqrG4 genes in the greater than 2.7 um fraction	dimensionless	no_bcodmo_term
sqrG4_dna_particulate_sd	standard deviation of the fraction of sqrG4 genes in the greater than 2.7 um fraction	dimensionless	std_dev
nirS_dna	copies of the nirS gene	x10^5/L	abundance
nirS_dna_sd	standard deviation of the copies of the nirS gene	x10^5/L	std_dev
nirS_dna_particulate	fraction of nirS genes in the greater than 2.7 um fraction	dimensionless	no_bcodmo_term
nirS_dna_particulate_sd	standard deviation of the fraction of nirS genes in the greater than 2.7 um fraction	dimensionless	std_dev
hzo_dna	copies of the hzo gene	x10^5/L	abundance
hzo_dna_sd	standard deviation of the copies of the hzo gene	x10^5/L	std_dev
hzo_dna_particulate	fraction of hzo genes in the greater than 2.7 um fraction	dimensionless	no_bcodmo_term
hzo_dna_particulate_sd	standard deviation of the fraction of hzo genes in the greater than 2.7 um fraction	dimensionless	std_dev
dsrA_dna	copies of the dsrA gene	x10^7/L	abundance
dsrA_dna_sd	standard deviation of the copies of the dsrA gene	x10^7/L	std_dev
dsrA_dna_particulate	fraction of dsrA genes in the greater than 2.7 um fraction	dimensionless	no_bcodmo_term
dsrA_dna_particulate_sd	standard deviation of the fraction of dsrA genes in the greater than 2.7 um fraction	dimensionless	std_dev

Database

Contribute Data

Dataset: qPCR data from the Cariaco Meta-Omics Cruises
Deployment: CAR212_2

Dataset acquisition description

Dataset Processing Description

Database

Contribute Data

Dataset: qPCR data from the Cariaco Meta-Omics CruisesDeployment: CAR212_2

Dataset acquisition description

Dataset Processing Description

Dataset: qPCR data from the Cariaco Meta-Omics Cruises
Deployment: CAR212_2