Dataset: GenBank accessions

Name: GenBank accession numbers and links for microbial isolates from sediment samples collected in Paleochori Bay, Milos Island, Greece during 2012 (Hydrothermal Autotrophic Carbon Fixation project)
Published: 2016-06-28
Keywords: biota, oceans

Cite This Dataset

Project:

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

Program:

Center for Dark Energy Biosphere Investigations (C-DEBI)

Principal Investigator:

Costantino Vetriani (Rutgers University, Rutgers IMCS)

BCO-DMO Data Manager:

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

Version Date:

2016-06-28

Restricted:

Validated:

Yes

Current State:

Final with updates expected

GenBank accession numbers and links for microbial isolates from sediment samples collected in Paleochori Bay, Milos Island, Greece during 2012 (Hydrothermal Autotrophic Carbon Fixation project)

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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

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

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

Data Files

File
GenBank_acc.csv (Comma Separated Values (.csv), 16.87 KB) MD5:a915ea94045b9cc90289f1ec43e87c65 Primary data file for dataset ID 650224

More Information about this dataset

Funding Sources

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

Deployments

Deployment	Synonyms	Start Date	Platform	Investigator
Milos_vents_2012		2012-05-21	shoreside Milos_vents	Dionysis Foustoukos (Co-Principal Investigator) Stefan M. Sievert (Co-Principal Investigator) Costantino Vetriani (Co-Principal Investigator)	data info

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

Date and time formats are described in python strftime() syntax.

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

Status message

Database

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Dataset: GenBank accessions