Dataset: OC1703A Sediment nifH amplicon sequences

Name: NCBI accession numbers describing nifH amplicon sequences from sediment samples collected offshore of San Francisco, Califronia, USA in March 2017 on R/V Oceanus cruise OC1703A
Published: 2021-10-13
Keywords: oceans

Cite This Dataset

DOI:10.26008/1912/bco-dmo.863192.1

Spatial Extent: N:37.134378 E:-122.544233 S:35.68905 W:-124.92211

Project:

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

Principal Investigator:

Anne E. Dekas (Stanford University)

BCO-DMO Data Manager:

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

Version:

Version Date:

2021-10-13

Restricted:

Validated:

Yes

Current State:

Final no updates expected

NCBI accession numbers describing nifH amplicon sequences from sediment samples collected offshore of San Francisco, Califronia, USA in March 2017 on R/V Oceanus cruise OC1703A

Abstract:

These data are raw, demultiplexed nifH amplicon sequences generated from Illumina MiSeq for the investigation of potential diazotroph diversity along a continental margin transect. Raw Illumina MiSeq 2×250 bp sequence data can be accessed in the NCBI SRA database under accession numbers ERP130242 and ERP120468 and BioProject accession numbers PRJEB46054 and PRJEB37167. Data under accession number ERP120468 and BioProject accession number PRJEB37167 were published in Kapili and Dekas, 2021. The generation of these data was completed on June 29, 2021.

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Archival Copy

Version Date	Archive	Persistent Identifier (PID)	Date PID Issued
2021-10-13	Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)	10.26008/1912/bco-dmo.863192.1	2022-08-31

Methods & Sampling

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

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

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

Data Files

File
nifH_amplicons.csv (Comma Separated Values (.csv), 62.29 KB) MD5:bb978997ab2d8ebe08aa42663aadd333 Primary data file for dataset ID 863192

More Information about this dataset

Funding Sources

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

Deployments

Deployment	Synonyms	Start Date	Platform	Investigator
OC1703A		2017-03-14	R/V Oceanus	Anne E. Dekas (Chief Scientist)	data info

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

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

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

Status message

Database

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Dataset: OC1703A Sediment nifH amplicon sequences