Dataset: Gill 16S rRNA amplicon sequencing

Name: GenBank Short Read Archive (SRA) sequence accession numbers for 16S rRNA gene amplicon in the Eastern Lau Spreading Center, Lau Basin from R/V Falkor from March to April 2016
Published: 2019-05-10
Keywords: oceans

View Data: Data not available yet

Cite This Dataset

Spatial Extent: N:-15.16 E:-173.57 S:-21.99 W:-176.57

Temporal Extent: 2016-03-27 - 2016-04-30

Project:

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

Principal Investigator:

Roxanne Beinart (Woods Hole Oceanographic Institution, WHOI)

BCO-DMO Data Manager:

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

Version:

Version Date:

2019-05-10

Restricted:

Validated:

Current State:

Data not available

GenBank Short Read Archive (SRA) sequence accession numbers for 16S rRNA gene amplicon in the Eastern Lau Spreading Center, Lau Basin from R/V Falkor from March to April 2016

Expand/Collapse All

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

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

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

Funding Sources

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

Deployments

Deployment	Synonyms	Start Date	Platform	Investigator
FK160407		2016-04-07	R/V Falkor	Charles Fisher (Chief Scientist) Peter Girguis (Chief Scientist)	data info

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

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

Supplied Name	Supplied description	Supplied Units	Standard Name
lat	latitude positive northward	decimal degrees	lat
lon	longitude positive eastward	decimal degrees	lon
Depth	depth	meters (m)	depth
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
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
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

Status message

Database

Contribute Data

Dataset: Gill 16S rRNA amplicon sequencing