Dataset: Alviniconcha gill transcriptomes
Deployment: FK160407

GenBank Short Read Archive (SRA) sequence accession numbers metatranscriptomic data from the gills of Alviniconcha species from R/V Falkor in the Eastern Lau Spreading Center, Lau Basin

View Data: For data, See Dataset Metadata Page: https://www.bco-dmo.org/dataset/767265

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)

Version:

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Description

GenBank Short Read Archive (SRA) sequence accession numbers metatranscriptomic data from the gills of Alviniconcha species

Methods & Sampling

Dataset acquisition description

Gill tissue pieces were quickly excised and homogenized in Trizol preservative using a Tissue-Tearor. Homogenates were stored at -80C until extraction with the Direct-zol RNA extraction kit (Zymo Research, Inc.). RNA was sequenced with Illumina NovaSeq using the RNAtag-Seq method with rRNA-depletion.

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
- converted date from m/d/yy to yyyy-mm-dd ISO convention

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

None available yet

Database

Contribute Data

Dataset: Alviniconcha gill transcriptomes
Deployment: FK160407

Dataset acquisition description

Dataset Processing Description

Database

Contribute Data

Dataset: Alviniconcha gill transcriptomesDeployment: FK160407

Dataset acquisition description

Dataset Processing Description

Dataset: Alviniconcha gill transcriptomes
Deployment: FK160407