Dataset: GenBank accessions
Deployment: Milos_vents_2012

GenBank accession numbers and links for microbial isolates from sediment samples collected at Paleochori Bay, Milos island, Greece

Principal Investigator:

Costantino Vetriani (Rutgers University, Rutgers IMCS)

BCO-DMO Data Manager:

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

Project:

Autotrophic carbon fixation at a shallow-water hydrothermal system: Constraining microbial activity, isotopic and geochemical regimes (Hydrothermal Autotrophic Carbon Fixation)

Current State:

Final with updates expected

Version Date:

2016-06-28

Data URL:

https://www.bco-dmo.org/dataset-deployment/650229/data

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Description

This dataset includes links to GenBank accession pages for microbial sequences collected at Milos Island.

Related Datasets:
Microbial isolates
Sample log

Methods & Sampling

Dataset acquisition description

Samples were collected at the shallow-water hydrothermal vent sites at Paleochori Bay, Milos Island, Greece. Sequence data (bacterial ssrRNA) was obtained using the Ion Torrent platform from total RNA extracted from 32 sediment and microbial biofilm samples characterized along a transect. Sequence data are currently being generated and analyzed, they will be deposited in GenBank prior to publication and will be made available to the scientific community.

Data Processing Description

Dataset Processing Description

BCO-DMO Processing:

- added conventional header with dataset name, PI name, version date, reference information
- renamed parameters to BCO-DMO standard
- created links to GenBank accession pages

More information about this dataset deployment

Funding

Award Number	Funding Source
OCE-1124141	NSF Division of Ocean Sciences

Instruments

Automated DNA Sequencer

Supplied Name:

Supplied Description:

Ion Torrent platform

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.

Push Corer

Supplied Name:

Supplied Description:

push cores were collected by SCUBA divers

Instrument Type

Generic Name: Push Corer

Generic Description:

Capable of being performed in numerous environments, push coring is just as it sounds. Push coring is simply pushing the core barrel (often an aluminum or polycarbonate tube) into the sediment by hand. A push core is useful in that it causes very little disturbance to the more delicate upper layers of a sub-aqueous sediment.

Description obtained from: http://web.whoi.edu/coastal-group/about/how-we-work/field-methods/coring/

Parameters

Supplied Name	Supplied description	Supplied Units	Standard Name
sample	sample: species name or source material	unitless	sample
analysis	type of genetic analysis	unitless	no_bcodmo_term
description	description of product	unitless	brief_desc
database	name of repository	unitless	no_bcodmo_term
GenBank_acc	GenBank accession number	unitless	accession_number
reference_paper	reference	unitless	reference_paper

Database

Contribute Data

Dataset: GenBank accessions
Deployment: Milos_vents_2012

Dataset acquisition description

Dataset Processing Description

Database

Contribute Data

Dataset: GenBank accessionsDeployment: Milos_vents_2012

Dataset acquisition description

Dataset Processing Description

Dataset: GenBank accessions
Deployment: Milos_vents_2012