Dataset: Community 16S rRNA gene sequences
Deployment: Lipp_2014-16

16S rRNA accessions

View Data: For data, See Dataset Metadata Page: https://osprey.bco-dmo.org/dataset/739077

Principal Investigator:

Erin K. Lipp (University of Georgia, UGA)

Co-Principal Investigator:

Elizabeth Ottesen (University of Georgia, UGA)

BCO-DMO Data Manager:

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

Project:

Vibrio as a model microbe for opportunistic heterotrophic response to Saharan dust deposition events in marine waters (Vibrio-dust deposition)

Version:

Expand/Collapse All

Description

This dataset includes NCBI GenBank accession from 2015 and 2016 field collections and experiments using Saharan source material and water from the lower Florida Keys to create microcosms for natural seawater communities. For full details, see (Westrich et al., 2016).

Methods & Sampling

Dataset acquisition description

Samples were collected as part of collections and experiments conducted at Looe Key reef microcosm experiments (2015 and 2016) and field collections (2016) in the Florida Keys National Marine Sanctuary (as described in other datasets with this project).

Samples (1 L) were prefiltered (2 um), concentrated on to 0.22 um filters, DNA extracted, and 16S rRNA in the V4 region amplified using 515F/806R primers with barcodes on both ends. Sequencing was conducted using Illumina MiSeq paired-end 250 chemistry.

Data Processing Description

Dataset Processing Description

BCO-DMO Processing Notes:
- added conventional header with dataset name, PI name, version date
- modified parameter names to conform with BCO-DMO naming conventions
- added links to NCBI BioProject pages

More information about this dataset deployment

Funding

Award Number	Funding Source
OCE-1357423	NSF Division of Ocean Sciences

Instruments

Automated DNA Sequencer

Supplied Name: Illumina MiSeq

Supplied Description:

Instrument Type

Generic Name: Automated DNA Sequencer

Acronym: Automated Sequencer

Generic Description:

General term for a laboratory instrument used for deciphering the order of bases in a strand of DNA. Sanger sequencers detect fluorescence from different dyes that are used to identify the A, C, G, and T extension reactions. Contemporary or Pyrosequencer methods are based on detecting the activity of DNA polymerase (a DNA synthesizing enzyme) with another chemoluminescent enzyme. Essentially, the method allows sequencing of a single strand of DNA by synthesizing the complementary strand along it, one base pair at a time, and detecting which base was actually added at each step.

Thermal Cycler

Supplied Name:

Supplied Description:

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
BioProject	NCBI GenBank BioProject accession number	unitless	accession_number
study	type of study	unitless	exp_type
sample_description	description of samples	unitless	sample_descrip
year	year of sample collection	unitless	year
num_sequences	number of sequences	unitless	count
NCBI_link	link to BioProject page at NCBI GenBank	unitless	external_link

Database

Contribute Data

Dataset: Community 16S rRNA gene sequences
Deployment: Lipp_2014-16

Dataset acquisition description

Dataset Processing Description

Database

Contribute Data

Dataset: Community 16S rRNA gene sequencesDeployment: Lipp_2014-16

Dataset acquisition description

Dataset Processing Description

Dataset: Community 16S rRNA gene sequences
Deployment: Lipp_2014-16