Dataset: RTqPCR data from the Cariaco Meta-Omics cruises
Deployment: CAR216_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://www.bco-dmo.org/dataset-deployment/652508/data

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Description

Quantitative reverse transcription polymerase chain reaction (RTqPCR) data collected from RNA samples on 1 leg of each of the CAR212 and CAR216 cruises.

Methods & Sampling

Dataset acquisition description

All samples were collected via a Microbial Sampler in situ Incubation Device (MS-SID).

RNA samples for RTqPCR were size-fractionated during collection by the MS-SID into a 2.7um fraction and 0.2-2.7um fraction using using a glass fiber filter pre filter in-line with 0.2um polysulfone filter membrane. RNA was preserved with RNAlater, stored frozen, and transported back to the home laboratory. RNA was extracted according to Stewart et al. (2012) using the mirVana miRNA Isolation kit (Ambion), purified with the RNeasy MinElute Cleanup kit (Qiagen), and reverse-transcribed to cDNA with the QuantiTect Reverse Transcription kit (Qiagen). RTqPCR assays were then carried in the same manner as qPCR assays.

Data Processing Description

Dataset Processing Description

All data were normalized to volume of seawater.

DMO Notes:

-transferred each RTqPCR 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

Submersible Incubation Device-In Situ Microbial Sampler

Supplied Name: Microbial Sampler in situ Incubation Device (MS-SID)

Supplied Description:

Samples size-fractionated during collection by the MS-SID

Instrument Type

Generic Name: Submersible Incubation Device-In Situ Microbial Sampler

Acronym: SID-ISMS

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/82/

Generic Description:

The Submersible Incubation Device-In Situ Microbial Sampler (SID-ISMS) system was developed for the 2011 NSF funded DHAB Metazoans Mediterranean Brine research project and first used on cruise AT18-14. The system includes several integrated components including: a 2 liter incubation chamber; fixation filters and water sample bottles; a High Range CTD (Neil Brown Ocean Sensors, Inc., USA) equipped with two turbidity sensors (Wet Labs ECOView); an Aanderra 2808F oxygen optode; an SDSL-data link; and a sonardyne beacon, a pinger and a 24 volt deep-sea battery. The sensors and sampling devices are mounted on a frame that is attached to the hydro-wire. Lowering rate and recovery speed are controlled by a winch mounted on the surface vessel.

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_rna	copies of the bacterial 16S gene	x10^7/L	abundance
bac16S_rna_sd	standard deviation of the copies of the bacterial 16S gene	x10^7/L	std_dev
bac16S_rna_particulate	fraction of bacterial 16S genes in the greater than 2.7 um fraction	dimensionless	no_bcodmo_term
bac16S_rna_particulate_sd	standard deviation of the fraction of bacterial 16S genes in the greater than 2.7 um fraction	dimensionless	std_dev
arch16S_rna	copies of the archaeal 16S gene	x10^8/L	abundance
arch16S_rna_sd	standard deviation of the copies of the archaeal 16S gene	x10^8/L	std_dev
arch16S_rna_particulate	fraction of archaeal 16S genes in the greater than 2.7 um fraction	dimensionless	no_bcodmo_term
arch16S_rna_particulate_sd	standard deviation of the fraction of archaeal 16S genes in the greater than 2.7 um fraction	dimensionless	std_dev
sqrG1_rna	copies of the sqrG1 gene	x10^3/L	abundance
sqrG1_rna_sd	standard deviation of the copies of the sqrG1 gene	x10^3/L	std_dev
sqrG1_rna_particulate	fraction of sqrG1 genes in the greater than 2.7 um fraction	dimensionless	no_bcodmo_term
sqrG1_rna_particulate_sd	standard deviation of the fraction of sqrG1 genes in the greater than 2.7 um fraction	dimensionless	std_dev
sqrG4_rna	copies of the sqrG4 gene	x10^0/L	abundance
sqrG4_rna_sd	standard deviation of the copies of the sqrG4 gene	x10^0/L	std_dev
sqrG4_rna_particulate	fraction of sqrG4 genes in the greater than 2.7 um fraction	dimensionless	no_bcodmo_term
sqrG4_rna_particulate_sd	standard deviation of the fraction of sqrG4 genes in the greater than 2.7 um fraction	dimensionless	std_dev
nirS_rna	copies of the nirS gene	x10^3/L	abundance
nirS_rna_sd	standard deviation of the copies of the nirS gene	x10^3/L	std_dev
nirS_rna_particulate	fraction of nirS genes in the greater than 2.7 um fraction	dimensionless	no_bcodmo_term
nirS_rna_particulate_sd	standard deviation of the fraction of nirS genes in the greater than 2.7 um fraction	dimensionless	std_dev
hzo_rna	copies of the hzo gene	x10^3/L	abundance
hzo_rna_sd	standard deviation of the copies of the hzo gene	x10^3/L	std_dev
hzo_rna_particulate	fraction of hzo genes in the greater than 2.7 um fraction	dimensionless	no_bcodmo_term
hzo_rna_particulate_sd	standard deviation of the fraction of hzo genes in the greater than 2.7 um fraction	dimensionless	std_dev
dsrA_rna	copies of the dsrA gene	x10^5/L	abundance
dsrA_rna_sd	standard deviation of the copies of the dsrA gene	x10^5/L	std_dev
dsrA_rna_particulate	fraction of dsrA genes in the greater than 2.7 um fraction	dimensionless	no_bcodmo_term
dsrA_rna_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: RTqPCR data from the Cariaco Meta-Omics cruises
Deployment: CAR216_2

Dataset acquisition description

Dataset Processing Description

Database

Contribute Data

Dataset: RTqPCR data from the Cariaco Meta-Omics cruisesDeployment: CAR216_2

Dataset acquisition description

Dataset Processing Description

Dataset: RTqPCR data from the Cariaco Meta-Omics cruises
Deployment: CAR216_2