ERDDAP > info > bcodmo_dataset_700961

Grid DAP Data	Sub- set	Table DAP Data	Make A Graph	W M S	Source Data Files	Acces- sible	Title	Sum- mary	FGDC, ISO, Metadata	Back- ground Info	RSS	E mail	Institution	Dataset ID
	set	data	graph		files	public	[Metabarcoding zooplankton at station ALOHA: NCBI SRA accession numbers] - NCBI Sequence Read Archive (SRA) accession numbers for fastq sequence files for each zooplankton community sample (Plankton Population Genetics project) (Basin-scale genetics of marine zooplankton)		F   I   M	background			BCO-DMO	bcodmo_dataset_700961

The Dataset's Variables and Attributes

Row Type	Variable Name	Attribute Name	Data Type	Value
attribute	NC_GLOBAL	access_formats	String	.htmlTable,.csv,.json,.mat,.nc,.tsv,.esriCsv,.geoJson
attribute	NC_GLOBAL	acquisition_description	String	SAMPLE INFORMATION Sample identifiers include the following codes. MOCNESS tow FA3: Night sampling FA4: Day sampling Depth range: N1: 1500-1000m N2: 1000-700m N3: 700-500m N4: 500-300m N5: 300-200m N6: 200-150m N7: 150-100m N8: 100-50m N9: 50m-0m Wet-sieved zooplankton size fractions SF1: 0.2-0.5 mm SF2: 0.5-1.0 mm SF3: 1.0-2.0 mm
attribute	NC_GLOBAL	awards_0_award_nid	String	473046
attribute	NC_GLOBAL	awards_0_award_number	String	OCE-1255697
attribute	NC_GLOBAL	awards_0_data_url	String	http://www.nsf.gov/awardsearch/showAward?AWD_ID=1255697
attribute	NC_GLOBAL	awards_0_funder_name	String	NSF Division of Ocean Sciences
attribute	NC_GLOBAL	awards_0_funding_acronym	String	NSF OCE
attribute	NC_GLOBAL	awards_0_funding_source_nid	String	355
attribute	NC_GLOBAL	awards_0_program_manager	String	David L. Garrison
attribute	NC_GLOBAL	awards_0_program_manager_nid	String	50534
attribute	NC_GLOBAL	awards_1_award_nid	String	537990
attribute	NC_GLOBAL	awards_1_award_number	String	OCE-1338959
attribute	NC_GLOBAL	awards_1_data_url	String	http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1338959
attribute	NC_GLOBAL	awards_1_funder_name	String	NSF Division of Ocean Sciences
attribute	NC_GLOBAL	awards_1_funding_acronym	String	NSF OCE
attribute	NC_GLOBAL	awards_1_funding_source_nid	String	355
attribute	NC_GLOBAL	awards_1_program_manager	String	David L. Garrison
attribute	NC_GLOBAL	awards_1_program_manager_nid	String	50534
attribute	NC_GLOBAL	awards_2_award_nid	String	539716
attribute	NC_GLOBAL	awards_2_award_number	String	OCE-1029478
attribute	NC_GLOBAL	awards_2_data_url	String	http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1029478
attribute	NC_GLOBAL	awards_2_funder_name	String	NSF Division of Ocean Sciences
attribute	NC_GLOBAL	awards_2_funding_acronym	String	NSF OCE
attribute	NC_GLOBAL	awards_2_funding_source_nid	String	355
attribute	NC_GLOBAL	awards_2_program_manager	String	David L. Garrison
attribute	NC_GLOBAL	awards_2_program_manager_nid	String	50534
attribute	NC_GLOBAL	cdm_data_type	String	Other
attribute	NC_GLOBAL	comment	String	ALOHA Zooplankton metabarcoding: SRA PI: Erica Goetze data version: 07 Jun 2017
attribute	NC_GLOBAL	Conventions	String	COARDS, CF-1.6, ACDD-1.3
attribute	NC_GLOBAL	creator_email	String	info at bco-dmo.org
attribute	NC_GLOBAL	creator_name	String	BCO-DMO
attribute	NC_GLOBAL	creator_type	String	institution
attribute	NC_GLOBAL	creator_url	String	https://www.bco-dmo.org/
attribute	NC_GLOBAL	data_source	String	extract_data_as_tsv version 2.3 19 Dec 2019
attribute	NC_GLOBAL	date_created	String	2017-05-25T19:52:10Z
attribute	NC_GLOBAL	date_modified	String	2017-08-02T12:08:50Z
attribute	NC_GLOBAL	defaultDataQuery	String	&time<now
attribute	NC_GLOBAL	doi	String	10.1575/1912/bco-dmo.704665
attribute	NC_GLOBAL	Easternmost_Easting	double	-158.0
attribute	NC_GLOBAL	geospatial_lat_max	double	22.75
attribute	NC_GLOBAL	geospatial_lat_min	double	22.75
attribute	NC_GLOBAL	geospatial_lat_units	String	degrees_north
attribute	NC_GLOBAL	geospatial_lon_max	double	-158.0
attribute	NC_GLOBAL	geospatial_lon_min	double	-158.0
attribute	NC_GLOBAL	geospatial_lon_units	String	degrees_east
attribute	NC_GLOBAL	infoUrl	String	https://www.bco-dmo.org/dataset/700961
attribute	NC_GLOBAL	institution	String	BCO-DMO
attribute	NC_GLOBAL	instruments_0_acronym	String	Automated Sequencer
attribute	NC_GLOBAL	instruments_0_dataset_instrument_description	String	Illumina MiSeq using V3 chemistry (300-bp, paired-end)
attribute	NC_GLOBAL	instruments_0_dataset_instrument_nid	String	700970
attribute	NC_GLOBAL	instruments_0_description	String	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.
attribute	NC_GLOBAL	instruments_0_instrument_name	String	Automated DNA Sequencer
attribute	NC_GLOBAL	instruments_0_instrument_nid	String	649
attribute	NC_GLOBAL	instruments_0_supplied_name	String	Illumina MiSeq
attribute	NC_GLOBAL	instruments_1_acronym	String	Thermal Cycler
attribute	NC_GLOBAL	instruments_1_dataset_instrument_nid	String	700972
attribute	NC_GLOBAL	instruments_1_description	String	General term for a laboratory apparatus commonly used for performing polymerase chain reaction (PCR). 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. (adapted from http://serc.carleton.edu/microbelife/research_methods/genomics/pcr.html)
attribute	NC_GLOBAL	instruments_1_instrument_name	String	PCR Thermal Cycler
attribute	NC_GLOBAL	instruments_1_instrument_nid	String	471582
attribute	NC_GLOBAL	instruments_1_supplied_name	String	quantitative PCR by the Evolutionary Genetics Core Facility (Hawaii Institute of Marine Biology)
attribute	NC_GLOBAL	instruments_2_acronym	String	Bioanalyzer
attribute	NC_GLOBAL	instruments_2_dataset_instrument_nid	String	700971
attribute	NC_GLOBAL	instruments_2_description	String	A Bioanalyzer is a laboratory instrument that provides the sizing and quantification of DNA, RNA, and proteins. One example is the Agilent Bioanalyzer 2100.
attribute	NC_GLOBAL	instruments_2_instrument_name	String	Bioanalyzer
attribute	NC_GLOBAL	instruments_2_instrument_nid	String	626182
attribute	NC_GLOBAL	instruments_2_supplied_name	String	Agilent 2100 Bioanalyzer
attribute	NC_GLOBAL	keywords	String	accession, analysis, analysis_name, bco, bco-dmo, biological, bioproject, bioproject_accession, bioproject_link, biosample, biosample_accession, biosample_link, chemical, data, dataset, description, design, design_description, dmo, erddap, instrument, instrument_model, latitude, layout, library, library_ID, library_layout, library_selection, library_source, library_strategy, link, longitude, management, model, name, oceanography, office, platform, preliminary, selection, source, strategy, title
attribute	NC_GLOBAL	license	String	https://www.bco-dmo.org/dataset/700961/license
attribute	NC_GLOBAL	metadata_source	String	https://www.bco-dmo.org/api/dataset/700961
attribute	NC_GLOBAL	Northernmost_Northing	double	22.75
attribute	NC_GLOBAL	param_mapping	String	{'700961': {'lat': 'master - latitude', 'lon': 'master - longitude'}}
attribute	NC_GLOBAL	parameter_source	String	https://www.bco-dmo.org/mapserver/dataset/700961/parameters
attribute	NC_GLOBAL	people_0_affiliation	String	University of Hawaii
attribute	NC_GLOBAL	people_0_person_name	String	Erica Goetze
attribute	NC_GLOBAL	people_0_person_nid	String	473048
attribute	NC_GLOBAL	people_0_role	String	Principal Investigator
attribute	NC_GLOBAL	people_0_role_type	String	originator
attribute	NC_GLOBAL	people_1_affiliation	String	University of Hawaii
attribute	NC_GLOBAL	people_1_person_name	String	Erica Goetze
attribute	NC_GLOBAL	people_1_person_nid	String	473048
attribute	NC_GLOBAL	people_1_role	String	Contact
attribute	NC_GLOBAL	people_1_role_type	String	related
attribute	NC_GLOBAL	people_2_affiliation	String	Woods Hole Oceanographic Institution
attribute	NC_GLOBAL	people_2_affiliation_acronym	String	WHOI BCO-DMO
attribute	NC_GLOBAL	people_2_person_name	String	Amber York
attribute	NC_GLOBAL	people_2_person_nid	String	643627
attribute	NC_GLOBAL	people_2_role	String	BCO-DMO Data Manager
attribute	NC_GLOBAL	people_2_role_type	String	related
attribute	NC_GLOBAL	project	String	Plankton Population Genetics
attribute	NC_GLOBAL	projects_0_acronym	String	Plankton Population Genetics
attribute	NC_GLOBAL	projects_0_description	String	Description from NSF award abstract: Marine zooplankton show strong ecological responses to climate change, but little is known about their capacity for evolutionary response. Many authors have assumed that the evolutionary potential of zooplankton is limited. However, recent studies provide circumstantial evidence for the idea that selection is a dominant evolutionary force acting on these species, and that genetic isolation can be achieved at regional spatial scales in pelagic habitats. This RAPID project will take advantage of a unique opportunity for basin-scale transect sampling through participation in the Atlantic Meridional Transect (AMT) cruise in 2014. The cruise will traverse more than 90 degrees of latitude in the Atlantic Ocean and include boreal-temperate, subtropical and tropical waters. Zooplankton samples will be collected along the transect, and mitochondrial and microsatellite markers will be used to identify the geographic location of strong genetic breaks within three copepod species. Bayesian and coalescent analytical techniques will test if these regions act as dispersal barriers. The physiological condition of animals collected in distinct ocean habitats will be assessed by measurements of egg production (at sea) as well as body size (condition index), dry weight, and carbon and nitrogen content. The PI will test the prediction that ocean regions that serve as dispersal barriers for marine holoplankton are areas of poor-quality habitat for the target species, and that this is a dominant mechanism driving population genetic structure in oceanic zooplankton. Note: This project is funded by an NSF RAPID award. This RAPID grant supported the shiptime costs, and all the sampling reported in the AMT24 zooplankton ecology cruise report (PDF). Online science outreach blog at: https://atlanticplankton.wordpress.com
attribute	NC_GLOBAL	projects_0_end_date	String	2015-11
attribute	NC_GLOBAL	projects_0_geolocation	String	Atlantic Ocean, 46 N - 46 S
attribute	NC_GLOBAL	projects_0_name	String	Basin-scale genetics of marine zooplankton
attribute	NC_GLOBAL	projects_0_project_nid	String	537991
attribute	NC_GLOBAL	projects_0_start_date	String	2013-12
attribute	NC_GLOBAL	publisher_name	String	Biological and Chemical Oceanographic Data Management Office (BCO-DMO)
attribute	NC_GLOBAL	publisher_type	String	institution
attribute	NC_GLOBAL	sourceUrl	String	(local files)
attribute	NC_GLOBAL	Southernmost_Northing	double	22.75
attribute	NC_GLOBAL	standard_name_vocabulary	String	CF Standard Name Table v55
attribute	NC_GLOBAL	subsetVariables	String	latitude,longitude,bioproject_accession,title,library_strategy,library_source,library_selection,library_layout,platform,instrument_model,design_description,bioproject_link
attribute	NC_GLOBAL	summary	String	These data include sample information and accession links to sequence data at The National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA). This data submission consists of metabarcoding data for the zooplankton community in the epipelagic, mesopelagic and upper bathypelagic zones (0-1500m) of the North Pacific Subtropical Gyre. The goal of this study was to assess the hidden diversity present in zooplankton assemblages in midwaters, and detect vertical gradients in species richness, depth distributions, and community composition of the full zooplankton assemblage. Samples were collected in June 2014 from Station ALOHA (22.75, -158) using a 1 meter square Multiple Opening and Closing Nets and Environmental Sampling System (MOCNESS, 200um mesh), on R/V Falkor cruise FK140613. \u00a0Next generation sequence data (Illumina MiSeq, V3 chemistry, 300-bp paired-end) of the zooplankton assemblage derive from amplicons of the V1-V2 region of 18S rRNA (primers described in Fonseca et al. 2010). The data includes sequences and read count abundance information for molecular OTUs from both holoplanktonic and meroplanktonic taxa Related dataset containing OTU tables and fasta sequences (representative / most abundance read for each OTU): [Metabarcoding zooplankton at ](\\http://www.bco- dmo.org/dataset/700279\\)[station](\\http://www.bco- dmo.org/dataset/700279\\)[ ALOHA: OTU tables and ](\\http://www.bco- dmo.org/dataset/700279\\)[fasta](\\http://www.bco- dmo.org/dataset/700279\\)[ files](\\http://www.bco- dmo.org/dataset/700279\\)
attribute	NC_GLOBAL	title	String	[Metabarcoding zooplankton at station ALOHA: NCBI SRA accession numbers] - NCBI Sequence Read Archive (SRA) accession numbers for fastq sequence files for each zooplankton community sample (Plankton Population Genetics project) (Basin-scale genetics of marine zooplankton)
attribute	NC_GLOBAL	version	String	1
attribute	NC_GLOBAL	Westernmost_Easting	double	-158.0
attribute	NC_GLOBAL	xml_source	String	osprey2erddap.update_xml() v1.3
variable	analysis_name		String
attribute	analysis_name	bcodmo_name	String	sample_descrip
attribute	analysis_name	description	String	Descriptive name of analysis including percent clustering and subsampling or no subsampling
attribute	analysis_name	long_name	String	Analysis Name
attribute	analysis_name	units	String	unitless
variable	latitude		double
attribute	latitude	_CoordinateAxisType	String	Lat
attribute	latitude	_FillValue	double	NaN
attribute	latitude	actual_range	double	22.75, 22.75
attribute	latitude	axis	String	Y
attribute	latitude	bcodmo_name	String	latitude
attribute	latitude	colorBarMaximum	double	90.0
attribute	latitude	colorBarMinimum	double	-90.0
attribute	latitude	description	String	Latitude of sample site (Station ALOHA)
attribute	latitude	ioos_category	String	Location
attribute	latitude	long_name	String	Latitude
attribute	latitude	nerc_identifier	String	https://vocab.nerc.ac.uk/collection/P09/current/LATX/
attribute	latitude	standard_name	String	latitude
attribute	latitude	units	String	degrees_north
variable	longitude		double
attribute	longitude	_CoordinateAxisType	String	Lon
attribute	longitude	_FillValue	double	NaN
attribute	longitude	actual_range	double	-158.0, -158.0
attribute	longitude	axis	String	X
attribute	longitude	bcodmo_name	String	longitude
attribute	longitude	colorBarMaximum	double	180.0
attribute	longitude	colorBarMinimum	double	-180.0
attribute	longitude	description	String	Longitude of sample site (Station ALOHA)
attribute	longitude	ioos_category	String	Location
attribute	longitude	long_name	String	Longitude
attribute	longitude	nerc_identifier	String	https://vocab.nerc.ac.uk/collection/P09/current/LONX/
attribute	longitude	standard_name	String	longitude
attribute	longitude	units	String	degrees_east
variable	library_ID		String
attribute	library_ID	bcodmo_name	String	sample
attribute	library_ID	description	String	Short unique identifier for the sequencing library.
attribute	library_ID	long_name	String	Library ID
attribute	library_ID	nerc_identifier	String	https://vocab.nerc.ac.uk/collection/P02/current/ACYC/
attribute	library_ID	units	String	unitless
variable	bioproject_accession		String
attribute	bioproject_accession	bcodmo_name	String	accession number
attribute	bioproject_accession	description	String	NCBI BioProject identifier
attribute	bioproject_accession	long_name	String	Bioproject Accession
attribute	bioproject_accession	units	String	unitless
variable	biosample_accession		String
attribute	biosample_accession	bcodmo_name	String	accession number
attribute	biosample_accession	description	String	NCBI BioSample identifier
attribute	biosample_accession	long_name	String	Biosample Accession
attribute	biosample_accession	units	String	unitless
variable	title		String
attribute	title	bcodmo_name	String	sample_descrip
attribute	title	description	String	Short description that will identify the dataset on public pages.
attribute	title	long_name	String	Title
attribute	title	units	String	unitless
variable	library_strategy		String
attribute	library_strategy	bcodmo_name	String	sample_descrip
attribute	library_strategy	description	String	Amplicon = Sequencing of overlapping or distinct PCR or RT-PCR products
attribute	library_strategy	long_name	String	Library Strategy
attribute	library_strategy	units	String	unitless
variable	library_source		String
attribute	library_source	bcodmo_name	String	sample_descrip
attribute	library_source	description	String	Metagenomic = Mixed material from metagenome
attribute	library_source	long_name	String	Library Source
attribute	library_source	units	String	unitless
variable	library_selection		String
attribute	library_selection	bcodmo_name	String	sample_descrip
attribute	library_selection	description	String	PCR = Source material was selected by designed primers
attribute	library_selection	long_name	String	Library Selection
attribute	library_selection	units	String	unitless
variable	library_layout		String
attribute	library_layout	bcodmo_name	String	sample_descrip
attribute	library_layout	description	String	Paired-end or Single
attribute	library_layout	long_name	String	Library Layout
attribute	library_layout	units	String	unitless
variable	platform		String
attribute	platform	bcodmo_name	String	sample_descrip
attribute	platform	description	String	Sequencing platforms [Illumina]
attribute	platform	long_name	String	Platform
attribute	platform	units	String	unitless
variable	instrument_model		String
attribute	instrument_model	bcodmo_name	String	instrument
attribute	instrument_model	description	String	Illumina instrument and model used for sequencing
attribute	instrument_model	long_name	String	Instrument Model
attribute	instrument_model	units	String	unitless
variable	design_description		String
attribute	design_description	bcodmo_name	String	sample_descrip
attribute	design_description	description	String	Free-form description of the methods used to create the sequencing library; a brief materials and methods section.
attribute	design_description	long_name	String	Design Description
attribute	design_description	units	String	unitless
variable	bioproject_link		String
attribute	bioproject_link	bcodmo_name	String	unknown
attribute	bioproject_link	description	String	bioproject_link
attribute	bioproject_link	long_name	String	Bioproject Link
attribute	bioproject_link	units	String	unitless
variable	biosample_link		String
attribute	biosample_link	bcodmo_name	String	unknown
attribute	biosample_link	description	String	biosample_link
attribute	biosample_link	long_name	String	Biosample Link
attribute	biosample_link	units	String	unitless

The information in the table above is also available in other file formats (.csv, .htmlTable, .itx, .json, .jsonlCSV1, .jsonlCSV, .jsonlKVP, .mat, .nc, .nccsv, .tsv, .xhtml) via a RESTful web service.