Dataset: AT26-18_FLOCS_DNA16S

Name: 16S rRNA gene amplicon sequences from FLOCS experiments at the Juan de Fuca Ridge CORKs during August 2014.
Published: 2019-02-20
Keywords: oceans

View Data: Data not available yet

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Spatial Extent: N:47.45 E:-127.45 S:47.45 W:-127.45

Temporal Extent: 2014-08 - 2014-08

Project:

Collaborative Research: Completing single- and cross-hole hydrgeologic and microbial experiments: Juan de Fuca Flank (JdF Flank)

Program:

Center for Dark Energy Biosphere Investigations (C-DEBI)

Principal Investigator:

Beth N. Orcutt (Bigelow Laboratory for Ocean Sciences)

Co-Principal Investigator:

Gustavo Ramirez (University of Southern California, USC)

BCO-DMO Data Manager:

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

Version:

Version Date:

2019-02-20

Restricted:

Validated:

Yes

Current State:

Final no updates expected

16S rRNA gene amplicon sequences from FLOCS experiments at the Juan de Fuca Ridge CORKs during August 2014.

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Description

The DNA data from the Juan de Fuca project are publicly available through NCBI Short Read Archive under BioProject PRJNA472057; BioSample accession numbers: SAMN09228041- SAMN09228055

species: uncultivated marine metagenome

description of the types of sequences: Illumina amplicon sequences of the V1-V3 hypervariable region of the 16S rRNA gene

locations where species were collected: IODP holes U1301A, U1362A, and U1362B on the Juan de Fuca Ridge flank, 47.45N/127.45W

Methods & Sampling

Polished mineral chips were prepared and deployed as described in Fisher et al. 2011 (DOI: 10.2204/iodp.proc.327.107.2011). Mineral colonization experiments were recovered during cruise AT26-18 in August 2014 and processed as described in Orcutt et al. 2011 (DOI: 10.1038/ismej.2010.157). Approximately 6g of each substrate underwent total DNA extraction using the MOBIO PowerSoil® DNA Isolation Kit (MOBIO Laboratories, Inc.) with modification from manufacturer instructions to include a phenol:chloroform:isoamyl alcohol (24:25:1) extraction step. Each batch of samples included procedural blanks. Replicate extracts were pooled and concentrated to 100 μl with vacuum centrifugation (SavantTM DNA SpeedVacTM Concentrator). Concentrated extracts were cleaned with the CleanAll DNA/RNA Clean Up and Concentration Kit (Norgen Biotek Corp, Thorold, Canada) and eluted in 20-50 μl of PCR-grade water. Sequencing of the V1-V3 region of the 16S rRNA gene was performed by Research and Testing Laboratory (Lubbock, TX, USA) using the forward primer 28F (5′- GAG TTT GAT CNT GGC TCA G -3′) and reverse primer 388R (5’- TGC TGC CTC CCG TAG GAG T -3’) for Bacteria using 2 x 300 bp kits on the Illumina MiSeq platform.

Data Processing Description

BCO-DMO Processing Notes:
- Nothing to report

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-1260697
NSF Division of Ocean Sciences	OCE-1536539

Deployments

Deployment	Synonyms	Start Date	Platform	Investigator
AT26-18		2014-08-10	R/V Atlantis	C. Geoffrey Wheat (Chief Scientist) Keir Becker (Co-Chief Scientist) Jordan Clark (Co-Chief Scientist) Katrina Edwards (Co-Chief Scientist) Andrew Fisher (Co-Chief Scientist) Michael S. Rappé (Co-Chief Scientist)	data info

Instruments

Automated DNA Sequencer

Supplied Name: Illumina MiSeq

Supplied Description:

Concentrated extracts were cleaned with the CleanAll DNA/RNA Clean Up and Concentration Kit (Norgen Biotek Corp, Thorold, Canada) and eluted in 20-50 μl of PCR-grade water. Sequencing of the V1-V3 region of the 16S rRNA gene was performed by Research and Testing Laboratory (Lubbock, TX, USA) using the forward primer 28F (5′- GAG TTT GAT CNT GGC TCA G -3′) and reverse primer 388R (5’- TGC TGC CTC CCG TAG GAG T -3’) for Bacteria using 2 x 300 bp kits on the Illumina MiSeq 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.

Parameters

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Database

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Dataset: AT26-18_FLOCS_DNA16S