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
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

Status message

Database

Contribute Data

Dataset: Gill 16S rRNA amplicon sequencing