Dataset: Trichodesmium sequence accessions
Deployment: AE1409

GenBank Trichodesmium accessions and associated metadata

Principal Investigator:

Sonya T. Dyhrman (Lamont-Doherty Earth Observatory, LDEO)

Co-Principal Investigator:

Benjamin A.S. Van Mooy (Woods Hole Oceanographic Institution, WHOI)

BCO-DMO Data Manager:

Nancy Copley (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Project:

Dissolved Phosphorus Processing by Trichodesmium Consortia: Quantitative Partitioning, Role of Microbial Coordination, and Impact on Nitrogen Fixation (P Processing by Tricho)

Deployment Synonyms:

PABST

Data URL:

https://www.bco-dmo.org/dataset-deployment/716824/data

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Description

Trichodesmium field sample sequence data from the July 2015 SCOPE cruise (R/V Kilo Moana KM1513) in the NW Pacific, the May 2014 PABST cruise (R/V Atlantic Explorer AE1409) in the Sargasso Sea, and other cruises in March 2007, May 2008, and August 2012 in North and South Pacific Subtropical Gyres, the and North Atlantic Subtropical Gyre. Links to the NCBI GenBank BioProjects are provided.

The accessions and further associated metadata are reported at NCBI GenBank as:
PRJNA314461
PRJNA330990
PRJNA381915 - to be made publicly accessible by 2018-10-27

Methods & Sampling

Dataset acquisition description

BioProject PRJNA314461; cruises KM0703, X0804, KM1309:Sample acquisition and processing (pdf)

BioProject PRJNA330990; cruise AE1409: Sample acquisition and processing (pdf)

BioProject PRJNA381915; cruise KM1513: Sample acquisition and processing (pdf)

Data Processing Description

Dataset Processing Description

BCO-DMO Processing:
Added conventional header with dataset name, PI name, version date.
Modified parameter names to conform with BCO-DMO naming conventions.
Split lat_lon into separate latitude and longitude columns
Added columns: cruise_id, cruise_name
Added links to NCBI GenBank BioProject accession pages

More information about this dataset deployment

Funding

Award Number	Funding Source
OCE-1332912	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.

Plankton Net

Supplied Name: net

Supplied Description:

Used to collect Trichodesmium colonies.

Instrument Type

Generic Name: Plankton Net

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/22/

Generic Description:

A Plankton Net is a generic term for a sampling net that is used to collect plankton. It is used only when detailed instrument documentation is not available.

Thermal Cycler

Supplied Name:

Supplied Description:

Instrument Type

Generic Name: Thermal Cycler

Generic Description:

A thermal cycler or "thermocycler" is a general term for a type of laboratory apparatus, commonly used for performing polymerase chain reaction (PCR), that is capable of repeatedly altering and maintaining specific temperatures for defined periods of time. The device has a thermal block with holes where tubes with the PCR reaction mixtures can be inserted. The cycler then raises and lowers the temperature of the block in discrete, pre-programmed steps. They can also be used to facilitate other temperature-sensitive reactions, including restriction enzyme digestion or rapid diagnostics.

(adapted from http://serc.carleton.edu/microbelife/research_methods/genomics/pcr.html)

Parameters

Supplied Name	Supplied description	Supplied Units	Standard Name
cruise_id	official UNOLS cruise identifier	unitless	cruise_id
cruise_name	project cruise name	unitless	cruise_name
sample_name	sequencing facility sample identifier	unitless	sample
sample_title	laboratory sample identifier	unitless	sample
bioproject_accession	collection of biological data related to a single initiative	unitless	accession_number
organism	cyanobacterium used in this study	unitless	taxon
strain	population of organism that descends from a single organism or pure culture isolate; not applicable to this dataset	unitless	taxon
isolate	specific individual from which this sample was obtained; not applicable to this dataset	unitless	taxon
host	host organism; not applicable to this dataset	unitless	taxon
isolation_source	physical; environmental; geographic source of the sample	unitless	region
collection_date	date sample was obtained	year-month-day	date
geo_loc_name	geographical origin of the sample	unitless	region
sample_type	sample type such as: whole organism; mixed culture; cell culture; metagenomic assembly	unitless	sample_descrip
biomaterial_provider	laboratory and principal investigator where sample came from	unitless	laboratory
collected_by	laboratory and principal investigator where organism was isolated	unitless	laboratory
depth	vertical distance below the surface where sample was collected	meters	depth
env_biome	descriptor of the broad ecological context of sample	unitless	site_descrip
genotype	observed genotype; not applicable to this dataset	unitless	no_bcodmo_term
lat	sample collection latitude; north is positive	decimal degrees	lat
lon	sample collection longitude; east is positive	decimal degrees	lon
passage_history	duration of sample	not applicable	duration
samp_size	amount of sample collected	colonies	count
NCBI_accession_link	link to NCBI GenBank BioProject accession page	unitless	external_link

Database

Contribute Data

Dataset: Trichodesmium sequence accessions
Deployment: AE1409

Dataset acquisition description

Dataset Processing Description

Database

Contribute Data

Dataset: Trichodesmium sequence accessionsDeployment: AE1409

Dataset acquisition description

Dataset Processing Description

Dataset: Trichodesmium sequence accessions
Deployment: AE1409