Dataset: Coral nutrient addition - DNA sample metadata
Deployment: Baker_lab_2015

Nutrient DNA sample log

Principal Investigator:

Andrew Baker (University of Miami Rosenstiel School of Marine and Atmospheric Science, UM-RSMAS)

BCO-DMO Data Manager:

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

Project:

New insights into the response of reef corals to climate change using the symbiont to host cell ratio as a metric of bleaching susceptibility (Reef coral symbioses)

Current State:

Final no updates expected

Version:

2015-10-15

Version Date:

2015-10-15

Data URL:

https://www.bco-dmo.org/dataset-deployment/616033/data

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Description

This dataset includes the coral reef sample id's and their treatments with additional iron, nitrates, phosphorous and food. Coral species used were Montastraea cavernosa and Siderastrea siderea. This experimental study is being undertaken in tanks at the University of Miami.

Access to the DNA sample data themselves will be restricted until analysis is completed, typically within 2 years of collection.

Methods & Sampling

Dataset acquisition description

Coral tissue biopsies were taken from replicate, one-inch cores of Montastraea cavernosa as small scrapings along a polyp’s calyx wall using a razor blade. The samples were immediately placed into 300uL of 1% SDS in DNA Buffer in 1.5mL Eppendorf tubes and heated to 65°C for one hour, where they are now stable at room temperature. Small aliquots of this lysate are then removed for DNA extraction on as as-needed basis.

We retain archived lysates (consisting of SDS-lysed tissue and a small piece of skeleton) that are stable long-term (>18 years) at room temperature.

Data for this project will ultimately include symbiont:host cell ratios for these samples using a variety of Symbiodinium clade-specific probes. In addition, data may also include the results of ITS2 genotyping using Denaturing Gradient Gel Electrophoresis (DGGE). Additional data, such as environmental data collected by dataloggers during experiments or field deployments, may also be contributed.

Data Processing Description

Dataset Processing Description

BCO-DMO Processing:

- added conventional header with dataset name, PI name, version date
- renamed parameters to BCO-DMO standard
- reformatted dates from m/d/yy to yyyy-mm-dd
- replaced spaces with underscores

More information about this dataset deployment

Funding

Award Number	Funding Source
OCE-1358699	NSF Division of Ocean Sciences

Instruments

None available yet

Parameters

Supplied Name	Supplied description	Supplied Units	Standard Name
group	column added by BCO-DMO to enable structuring of the data	unitless	no_bcodmo_term
date	date of treatment application	yyyy-mm-dd	date
treatment	experimental treatment: Fe = addition of Iron; N = addition of Nitrates; P = addition of phosphates	unitless	treatment
tissue_sample	tissue sample identification code	unitless	sample
species_core_id	sample id: species code + core code + specimen number	unitless	sample

Database

Contribute Data

Dataset: Coral nutrient addition - DNA sample metadata
Deployment: Baker_lab_2015

Dataset acquisition description

Dataset Processing Description

Database

Contribute Data

Dataset: Coral nutrient addition - DNA sample metadataDeployment: Baker_lab_2015

Dataset acquisition description

Dataset Processing Description

Dataset: Coral nutrient addition - DNA sample metadata
Deployment: Baker_lab_2015