Dataset: Phytoflux_BATS DGGE gel images
Deployment: AE1003

Denaturing gradient gel electrophoresis images from eukaryotic and cyanobacterial samples.

Lead Principal Investigator:

Susanne Neuer (Arizona State University, ASU)

Co-Principal Investigator:

Michael W. Lomas (Bermuda Institute of Ocean Sciences, BIOS)

Student:

Jessica Amacher (Arizona State University, ASU)

BCO-DMO Data Manager:

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

Project:

Composition of the plankton community and its contribution to particle flux in the Sargasso Sea (Plankton particle flux)

Current State:

Final no updates expected

Deployment Synonyms:

255, GF255

Version Date:

2010-02-22

Data URL:

https://osprey.bco-dmo.org/dataset-deployment/455917/data

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Description

This dataset includes original denaturing gradient gel images that resulted in eukaryotic and cyanobacterial DNA sequence data obtained from the upper water column as well as from shallow drifting traps during regular BATS cruises from May 2008-April 2010. The associated dataset contains a complete list of denaturing gradient gel results and the closest sequence matches from the NCBI database for each excised band (phylotype).

Associated dataset: phytoflux_BATS

Methods & Sampling

Dataset acquisition description

Sampling and Analytical Methodology:
Sampling was conducted monthly from May 2008-April 2010 at the Bermuda Atlantic Time-Series (BATS). Samples were collected for DNA analysis from four depths in the upper water column and from 150 m particle traps. DNA was extracted from these samples and a region of the 18S ribosomal RNA gene for eukaryotes and 16S rRNA gene for cyanobacteria was amplified by PCR using eukaryotic and cyanobacterial primers. Each amplified sample was subjected to Denaturing Gradient Gel Electrophoresis in order to “fingerprint” the community. Individual bands were excised and identified by sequence matching using the NCBI database (http://blast.ncbi.nlm.nih.gov). Quantity One software package was used to determine similarity between samples. The efficiency of recovery was determined by qPCR in order to accurately calculate the DNA present in the water column and DNA flux into particle traps. For further detail please refer to:
Jessica Amacher, Susanne Neuer, Michael Lomas. Accepted. DNA-based molecular fingerprinting of the contribution of eukaryotic protists and cyanobacteria to particle flux at the Bermuda Atlantic Time-Series Study. Deep Sea Research part II.

Data Processing Description

Dataset Processing Description

Data Processing:
Denaturing gradient gels were imaged and analyzed with the BioRad Fluor-S imager. Bands were selected and matched manually for band matrices included in these data.

More information about this dataset deployment

Funding

Award Number	Funding Source
OCE-0752592	NSF Division of Ocean Sciences

Instruments

Sediment Trap

Supplied Description:

Standard BATS program trap: the regular 72 hr, fixed tubes deployment as well as a 24 hr, unfixed deployment.

Instrument Type

Generic Name: Sediment Trap

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/33/

Generic Description:

Sediment traps are specially designed containers deployed in the water column for periods of time to collect particles from the water column falling toward the sea floor. In general a sediment trap has a jar at the bottom to collect the sample and a broad funnel-shaped opening at the top with baffles to keep out very large objects and help prevent the funnel from clogging. This designation is used when the specific type of sediment trap was not specified by the contributing investigator.

Parameters

Supplied Name	Supplied description	Supplied Units	Standard Name
image_file	Link to the pdf containing the images contained in the dataset.	text	dataset_id

Database

Contribute Data

Dataset: Phytoflux_BATS DGGE gel images
Deployment: AE1003

Dataset acquisition description

Dataset Processing Description

Database

Contribute Data

Dataset: Phytoflux_BATS DGGE gel imagesDeployment: AE1003

Dataset acquisition description

Dataset Processing Description

Dataset: Phytoflux_BATS DGGE gel images
Deployment: AE1003