Dataset: Gill 16S rRNA amplicon sequencing
Deployment: FK160407

GenBank Short Read Archive (SRA) sequence accession numbers for 16S rRNA gene amplicon data from the gills of Alviniconcha species, Ifremeria nautilei, and Bathymodiolus septemdierum.

View Data: For data, See Dataset Metadata Page: https://osprey.bco-dmo.org/dataset/767230

Principal Investigator:

Roxanne Beinart (Woods Hole Oceanographic Institution, WHOI)

BCO-DMO Data Manager:

Mathew Biddle (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Project:

Collaborative Research: Ecosystem dynamics of Western Pacific hydrothermal vent communities associated with polymetallic sulfide deposits (Eco Dyn W Pacific Vents)

Current State:

Preliminary and in progress

Version:

Version Date:

2019-05-10

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Description

GenBank Short Read Archive (SRA) sequence accession numbers for 16S rRNA gene amplicon data from the gills of Alviniconcha species, Ifremeria nautilei, and Bathymodiolus septemdierum.

Methods & Sampling

Dataset acquisition description

Gill tissue pieces were excised and stored in RNALater (Invitrogen, Inc.) at -80C until DNA extraction. DNA was extracted using the Quick-DNA Plus kit (Zymo Research, Inc.). 16S rRNA genes were amplified from the extracted DNA with the 515F/926R primers (Walters et al., 2015) and PE 251bp reads were sequenced using Illumina MiSeq.

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 lat and lon columns
- added ISO_datetime column containing the date and time combined into ISO 8601 format

More information about this dataset deployment

Funding

Award Number	Funding Source
OCE-1536331	NSF Division of Ocean Sciences

Instruments

Automated DNA Sequencer

Supplied Name: Illumina MiSeq.

Supplied Description:

16S rRNA genes were amplified from the extracted DNA with the 515F/926R primers (Walters et al., 2015) and PE 251bp reads were sequenced using Illumina MiSeq.

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.

Parameters

Supplied Name	Supplied description	Supplied Units	Standard Name
Sample_ID	Sample ID	unitless	sample
Species	species	unitless	species
BioSample	biosample	unitless	no_bcodmo_term
BioProject	bioproject	unitless	no_bcodmo_term
SRA_Accession	Short Read Archive Accession	unitless	accession_number
SRA_Study	Short Read Archive study	unitless	no_bcodmo_term
Cruise	cruise	unitless	cruise_id
Collection_ID	collection ID	unitless	sample_descrip
Vent_field	vent field	unitless	site_descrip
Lat	latitude as a text string including hemisphere	unitless	lat
Lon	longitude as a text string including hemisphere	unitless	lon
Depth	depth	meters (m)	depth
Date	date in yyyy-mm-dd format	unitless	date
Time	time in hh:mm:ss format	unitless	time
ISO_datetime	date and time following ISO 8601 yyyy-mm-ddTHH:MM:ss	unitless	ISO_DateTime_UTC
lat	latitude positive northward	decimal degrees	lat
lon	longitude positive eastward	decimal degrees	lon

Database

Contribute Data

Dataset: Gill 16S rRNA amplicon sequencing
Deployment: FK160407

Dataset acquisition description

Dataset Processing Description

Database

Contribute Data

Dataset: Gill 16S rRNA amplicon sequencingDeployment: FK160407

Dataset acquisition description

Dataset Processing Description

Dataset: Gill 16S rRNA amplicon sequencing
Deployment: FK160407