Dataset: Sample log
Deployment: Milos_vents_2012

Metadata 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 no updates expected

Version Date:

2016-06-28

Data URL:

https://www.bco-dmo.org/dataset-deployment/650180/data

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Description

List of samples collected at the shallow-water hydrothermal vent sites at Paleochori Bay, Milos Island, Greece, and includes the sample description, collection distance from the vent, type and amount of nucleic acids.

Related Datasets:
GenBank accessions
Microbial isolates

Methods & Sampling

Dataset acquisition description

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

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
lat	latitude; north is positive	decimal degrees	lat
lon	longitude; east is positive	decimal degrees	lon
sample_description	type of sample: from sediment of microbial mat	unitless	sample_descrip
sample_id	sample identification	unitless	sample
dist_vent_cm	distance from vent center	cm	no_bcodmo_term
sampling_instr	instrument used to collect sample	unitless	instrument
preservation	sample preservative	unitless	no_bcodmo_term
core_depth	depth within the sediment core	cm	depth
date_collected	date sampled	unitless	date
nucleic_acid	nucleic acid extracted	unitless	no_bcodmo_term
nucleic_acid_conc_ng_ul	nucleic acid concentration	nanograms/microliter	no_bcodmo_term
cDNA_conc_ng_ul	cDNA concentration	nanograms/microliter	no_bcodmo_term

Database

Contribute Data

Dataset: Sample log
Deployment: Milos_vents_2012

Dataset acquisition description

Dataset Processing Description

Database

Contribute Data

Dataset: Sample logDeployment: Milos_vents_2012

Dataset acquisition description

Dataset Processing Description

Dataset: Sample log
Deployment: Milos_vents_2012