Dataset: OC1703A Sediment nifH amplicon sequences
Deployment: OC1703A

OC1703A Sediment nifH amplicon sequences

Principal Investigator:

Anne E. Dekas (Stanford University)

BCO-DMO Data Manager:

Shannon Rauch (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Project:

Nitrogen Fixation in Deep-Sea Sediments (Deep Sediment N Fix)

Data URL:

https://www.bco-dmo.org/dataset-deployment/863199/data

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Description

Methods & Sampling

Dataset acquisition description

Sediment samples were collected using a multicorer on board the R/V Oceanus (March 2017) and sample aliquots were immediately stored at -80°C until DNA extraction. DNA was extracted in the laboratory using an RNeasy PowerSoil DNA elution kit (Qiagen, catalog no. 12867-25) after RNA was extracted using an RNeasy PowerSoil Total RNA kit. (Qiagen, catalog no. 12866-25).

nifH sequences were amplified using the PCR primers described in Mehta et al., 2003 and amplicons were prepared for 2×250 bp sequencing on an Illumina MiSeq platform following the protocol described in Kapili et al., 2020.

Data Processing Description

Dataset Processing Description

Data Processing:
Samples were demultiplexed at the UC Davis DNA Technologies Core facility.

BCO-DMO Processing:
- replaced "na" with "nd" (no data)

More information about this dataset deployment

Funding

Award Number	Funding Source
OCE-1634297	NSF Division of Ocean Sciences

Instruments

Automated DNA Sequencer

Supplied Name: Illumina MiSeq platform

Supplied Description:

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.

Multi Corer

Supplied Name: MC-800

Supplied Description:

Instrument Type

Generic Name: Multi Corer

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/51/

Generic Description:

The Multi Corer is a benthic coring device used to collect multiple, simultaneous, undisturbed sediment/water samples from the seafloor. Multiple coring tubes with varying sampling capacity depending on tube dimensions are mounted in a frame designed to sample the deep ocean seafloor. For more information, see Barnett et al. (1984) in Oceanologica Acta, 7, pp. 399-408.

Parameters

Supplied Name	Supplied description	Supplied Units	Standard Name
BioProject	BioProject accession	unitless	BioProject
BioSample	BioSample accession	unitless	BioSample
SRA_study	SRA study accession	unitless	SRA_study
Assay_Type	Assay type	unitless	sampling_method
Sequencing_platform	Squencing platform	unitless	instrument
Instrument_model	Illumina model	unitless	instrument
Library_layout	Library layout	unitless	sampling_method
File_name_1	File name of forward reads	unitless	file_name
File_name_2	File name of reverse reads	unitless	file_name
File_type	File type	unitless	file_name
Sequencing_method	Sequencing method	unitless	sampling_method
Library_selection	Library selection	unitless	sampling_method
PCR_primers	PCR primer sequences	unitless	sequence
Sequencing_adapters	Illumina adapter sequences	unitless	sequence
Geographic_location	Sampling location	unitless	site
Sample_type	Environmental sample type	unitless	sample_type
Sample_name	Sample name	unitless	sample
Sample_latitude	Sampling latitude	decimal degrees North	lat
Sample_longitude	Sampling longitude	decimal degrees East	lon
Deployment_number	Deployment number	unitless	deploy
Multicore_number	Mulitcore number	unitless	core_id
Seawater_depth	Seawater depth	meters below sea surface	depth
Sediment_depth	Sediment depth	centimeters below sediment surface	depth_core

Database

Contribute Data

Dataset: OC1703A Sediment nifH amplicon sequences
Deployment: OC1703A

Dataset acquisition description

Dataset Processing Description

Database

Contribute Data

Dataset: OC1703A Sediment nifH amplicon sequencesDeployment: OC1703A

Dataset acquisition description

Dataset Processing Description

Dataset: OC1703A Sediment nifH amplicon sequences
Deployment: OC1703A