ERDDAP > info > bcodmo_dataset_768550

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	[DYEatom: Metatranscriptome accessions and assembled contigs] - DYEatom Metatranscriptome metadata from RV/Point Sur cruise PS1312 in the Monterey Bay area, June-July 2013 (Linking physiological and molecular aspects of diatom silicification in field populations)		F   I   M	background			BCO-DMO	bcodmo_dataset_768550

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	Water was collected using Niskin bottles mounted on a CTD rosette. Biomass for metatranscriptomic analysis was collected by filtration (after a 200 micron pre-filtration) onto 47 mm, 1.2-micron pore size polycarbonate filters at <5 psi for no longer than 15 min to minimize degradation. Filters were flash frozen in liquid nitrogen and stored at -80 degrees C. Upon analysis, filters were thawed and RNA was extracted using TRIzol reagent according to the manufacturer\u2019s protocol (Life Technologies). Metatranscriptome libraries were constructed using 500 ng of total RNA and a TruSeq RNA Sample Preparation Kit (Illumina; San Diego, CA) following the Low-Throughput protocol. The mean size of the final libraries was confirmed to be between 359-420 base pairs (bp) using an Agilent Bioanalyzer 2100 (Santa Clara, CA). Libraries were paired-end sequenced (2x150 bp) on the Illumina HiSeq platform. ORFs were annotated via BLASTP alignment (e-value > 10-3) to a comprehensive protein database, phyloDB, as well as screened for function de-novo by assigning Pfams, TIGRfams and transmembrane tmHMMs with hmmer 3.0 ([http://hmmer.org/](\\"http://hmmer.org/\\")). PhyloDB 1.076 consists of 24,509,327 peptides from 19,962 viral, 230 archaeal, 4,910 bacterial, and 894 eukaryotic taxa. It includes peptides at KEGG, GenBank, JGI, ENSEMBL, CAMERA, and various other repositories, as well as from the 410 taxa of the Marine Microbial Eukaryotic Transcriptome Sequencing Project. Taxonomic annotation of ORFs was also conducted via BLASTP to phyloDB. All cruise related data are available publicly at the Biological and Chemical Oceanography Data Management Office under project number 550825 ([https://www .bco-dmo.org/project/550825](\\"https://www.bco-dmo.org/project/550825\\")). The metatranscriptomic data have been deposited in the NCBI sequence read archive (BioProject accession no. PRJNA528986: BioSample accession nos. SAMN11263616 - SAMN11263639 and SAMN11258802-SAMN11258825). Assembled contigs used in this study can also be found at [https://scripps.ucsd.edu/labs/aallen/data/](\\"https://scripps.ucsd.edu/labs/aallen/data/\\"). Unassembled reads and rRNA data from this study:\u00a0[https://www.ncbi.nlm.nih.gov/bioproject/PRJNA528986](\\"https://www.ncbi.nlm.nih.gov/bioproject/PRJNA528986\\") Assembled contigs: See Supplemental Files.
attribute	NC_GLOBAL	awards_0_award_nid	String	558197
attribute	NC_GLOBAL	awards_0_award_number	String	OCE-1333929
attribute	NC_GLOBAL	awards_0_data_url	String	http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1333929
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	cdm_data_type	String	Other
attribute	NC_GLOBAL	comment	String	DYEatom Metatranscriptome from RV/Point Sur cruise PS1312, DYEatom cruise, June-July 2013 PI: K. Thamatrakoln (Rutgers) version date: 2019-05-29
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	2019-05-23T19:52:52Z
attribute	NC_GLOBAL	date_modified	String	2019-07-31T16:26:40Z
attribute	NC_GLOBAL	defaultDataQuery	String	&amp;time&lt;now
attribute	NC_GLOBAL	doi	String	10.1575/1912/bco-dmo.768550.1
attribute	NC_GLOBAL	Easternmost_Easting	double	-121.981
attribute	NC_GLOBAL	geospatial_lat_max	double	38.265
attribute	NC_GLOBAL	geospatial_lat_min	double	36.455
attribute	NC_GLOBAL	geospatial_lat_units	String	degrees_north
attribute	NC_GLOBAL	geospatial_lon_max	double	-121.981
attribute	NC_GLOBAL	geospatial_lon_min	double	-123.969
attribute	NC_GLOBAL	geospatial_lon_units	String	degrees_east
attribute	NC_GLOBAL	geospatial_vertical_max	double	55.5
attribute	NC_GLOBAL	geospatial_vertical_min	double	1.6
attribute	NC_GLOBAL	geospatial_vertical_positive	String	down
attribute	NC_GLOBAL	geospatial_vertical_units	String	m
attribute	NC_GLOBAL	infoUrl	String	https://www.bco-dmo.org/dataset/768550
attribute	NC_GLOBAL	institution	String	BCO-DMO
attribute	NC_GLOBAL	instruments_0_acronym	String	Automated Sequencer
attribute	NC_GLOBAL	instruments_0_dataset_instrument_nid	String	768559
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 HiSeq platform
attribute	NC_GLOBAL	keywords	String	accession, bco, bco-dmo, bio, biological, BioProject_id, BioProject_type, BioSample, cast, chemical, collection, conductivity, cruise, cruise_id, ctd, CTD_cast, data, dataset, date, depth, depth_m, dmo, erddap, latitude, longitude, management, name, oceanography, office, package, Package_type, preliminary, project, sample, Sample_name, sonde, sra, SRA_id, station, temperature, time, type, version
attribute	NC_GLOBAL	license	String	https://www.bco-dmo.org/dataset/768550/license
attribute	NC_GLOBAL	metadata_source	String	https://www.bco-dmo.org/api/dataset/768550
attribute	NC_GLOBAL	Northernmost_Northing	double	38.265
attribute	NC_GLOBAL	param_mapping	String	{'768550': {'Lat': 'flag - latitude', 'depth_m': 'flag - depth', 'Long': 'flag - longitude'}}
attribute	NC_GLOBAL	parameter_source	String	https://www.bco-dmo.org/mapserver/dataset/768550/parameters
attribute	NC_GLOBAL	people_0_affiliation	String	Rutgers University
attribute	NC_GLOBAL	people_0_affiliation_acronym	String	Rutgers IMCS
attribute	NC_GLOBAL	people_0_person_name	String	Kimberlee Thamatrakoln
attribute	NC_GLOBAL	people_0_person_nid	String	558200
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	J. Craig Venter Institute
attribute	NC_GLOBAL	people_1_affiliation_acronym	String	JCVI
attribute	NC_GLOBAL	people_1_person_name	String	Andrew E Allen
attribute	NC_GLOBAL	people_1_person_nid	String	51525
attribute	NC_GLOBAL	people_1_role	String	Co-Principal Investigator
attribute	NC_GLOBAL	people_1_role_type	String	originator
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	Nancy Copley
attribute	NC_GLOBAL	people_2_person_nid	String	50396
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	Diatom Silicification
attribute	NC_GLOBAL	projects_0_acronym	String	Diatom Silicification
attribute	NC_GLOBAL	projects_0_description	String	Description from NSF award abstract: Diatoms, unicellular, eukaryotic photoautotrophs, are among the most ecologically successful and functionally diverse organisms in the ocean. In addition to contributing one-fifth of total global primary productivity, diatoms are also the largest group of silicifying organisms in the ocean. Thus, diatoms form a critical link between the carbon and silicon (Si) cycles. The goal of this project is to understand the molecular regulation of silicification processes in natural diatom populations to better understand the processes controlling diatom productivity in the sea. Through culture studies and two research cruises, this research will couple classical measurements of silicon uptake and silica production with molecular and biochemical analyses of Silicification-Related Gene (SiRG) and protein expression. The proposed cruise track off the West Coast of the US will target gradients in Si and iron (Fe) concentrations with the following goals: 1) Characterize the expression pattern of SiRGs, 2) Correlate SiRG expression patterns to Si concentrations, silicon uptake kinetics, and silica production rates, 3) Develop a method to normalize uptake kinetics and silica production to SiRG expression levels as a more accurate measure of diatom activity and growth, 4) Characterize the diel periodicity of silica production and SiRG expression. It is estimated that diatoms process 240 Teramoles of biogenic silica each year and that each molecule of silicon is cycled through a diatom 39 times before being exported to the deep ocean. Decades of oceanographic and field research have provided detailed insight into the dynamics of silicon uptake and silica production in natural populations, but a molecular understanding of the factors that influence silicification processes is required for further understanding the regulation of silicon and carbon fluxes in the ocean. Characterizing the genetic potential for silicification will provide new information on the factors that regulate the distribution of diatoms and influence in situ rates of silicon uptake and silica production. This research is expected to provide significant information about the molecular regulation of silicification in natural populations and the physiological basis of Si limitation in the sea.
attribute	NC_GLOBAL	projects_0_end_date	String	2016-08
attribute	NC_GLOBAL	projects_0_geolocation	String	Oregon/California Coastal Upwelling Zone, between 34-44N and 120-124W
attribute	NC_GLOBAL	projects_0_name	String	Linking physiological and molecular aspects of diatom silicification in field populations
attribute	NC_GLOBAL	projects_0_project_nid	String	558198
attribute	NC_GLOBAL	projects_0_start_date	String	2013-09
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	36.455
attribute	NC_GLOBAL	standard_name_vocabulary	String	CF Standard Name Table v55
attribute	NC_GLOBAL	subsetVariables	String	BioProject_type,BioProject_id,Package_type,version,cruise_id
attribute	NC_GLOBAL	summary	String	Metadata for assembled contigs and ORFS from metatranscriptome analysis from CTD casts in the Monterey Bay area on RV/Point Sur cruise PS1312, June-July 2013. Assembled contigs files are also available; see Supplemental Files.
attribute	NC_GLOBAL	title	String	[DYEatom: Metatranscriptome accessions and assembled contigs] - DYEatom Metatranscriptome metadata from RV/Point Sur cruise PS1312 in the Monterey Bay area, June-July 2013 (Linking physiological and molecular aspects of diatom silicification in field populations)
attribute	NC_GLOBAL	version	String	1
attribute	NC_GLOBAL	Westernmost_Easting	double	-123.969
attribute	NC_GLOBAL	xml_source	String	osprey2erddap.update_xml() v1.3
variable	BioProject_type		String
attribute	BioProject_type	bcodmo_name	String	exp_type
attribute	BioProject_type	description	String	NCBI BioProject type
attribute	BioProject_type	long_name	String	Bio Project Type
attribute	BioProject_type	units	String	unitless
variable	BioProject_id		String
attribute	BioProject_id	bcodmo_name	String	exp_id
attribute	BioProject_id	description	String	NCBI BioProject identifier
attribute	BioProject_id	long_name	String	Bio Project Id
attribute	BioProject_id	units	String	unitless
variable	BioSample		String
attribute	BioSample	bcodmo_name	String	accession number
attribute	BioSample	description	String	NCBI BioSample identifier
attribute	BioSample	long_name	String	Bio Sample
attribute	BioSample	units	String	unitless
variable	Sample_name		String
attribute	Sample_name	bcodmo_name	String	sample
attribute	Sample_name	description	String	NCBI Sample identifier
attribute	Sample_name	long_name	String	Sample Name
attribute	Sample_name	nerc_identifier	String	https://vocab.nerc.ac.uk/collection/P02/current/ACYC/
attribute	Sample_name	units	String	unitless
variable	SRA_id		String
attribute	SRA_id	bcodmo_name	String	sample
attribute	SRA_id	description	String	NCBI SRA identifier
attribute	SRA_id	long_name	String	SRA Id
attribute	SRA_id	nerc_identifier	String	https://vocab.nerc.ac.uk/collection/P02/current/ACYC/
attribute	SRA_id	units	String	unitless
variable	Package_type		String
attribute	Package_type	bcodmo_name	String	sample_type
attribute	Package_type	description	String	NCBI Package type
attribute	Package_type	long_name	String	Package Type
attribute	Package_type	units	String	unitless
variable	version		byte
attribute	version	_FillValue	byte	127
attribute	version	actual_range	byte	1, 1
attribute	version	bcodmo_name	String	unknown
attribute	version	description	String	NCBI version
attribute	version	long_name	String	Version
attribute	version	units	String	unitless
variable	Accession		String
attribute	Accession	bcodmo_name	String	accession number
attribute	Accession	description	String	NCBI Accession
attribute	Accession	long_name	String	Accession
attribute	Accession	units	String	unitless
variable	ID		int
attribute	ID	_FillValue	int	2147483647
attribute	ID	actual_range	int	11258802, 11263639
attribute	ID	bcodmo_name	String	accession number
attribute	ID	description	String	NCBI ID
attribute	ID	long_name	String	ID
attribute	ID	units	String	unitless
variable	cruise_id		String
attribute	cruise_id	bcodmo_name	String	cruise_id
attribute	cruise_id	description	String	cruise identifier
attribute	cruise_id	long_name	String	Cruise Id
attribute	cruise_id	units	String	unitless
variable	CTD_cast		String
attribute	CTD_cast	bcodmo_name	String	cast
attribute	CTD_cast	description	String	CTD cast number
attribute	CTD_cast	long_name	String	CTD Cast
attribute	CTD_cast	units	String	unitless
variable	latitude		double
attribute	latitude	_CoordinateAxisType	String	Lat
attribute	latitude	_FillValue	double	NaN
attribute	latitude	actual_range	double	36.455, 38.265
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; north is positive
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	-123.969, -121.981
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; east is positive
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	source_name	String	Long
attribute	longitude	standard_name	String	longitude
attribute	longitude	units	String	degrees_east
variable	Date_collection		String
attribute	Date_collection	bcodmo_name	String	date
attribute	Date_collection	description	String	date of collection; formatted as yyyy-mm-dd
attribute	Date_collection	long_name	String	Date Collection
attribute	Date_collection	nerc_identifier	String	https://vocab.nerc.ac.uk/collection/P01/current/ADATAA01/
attribute	Date_collection	source_name	String	Date_collection
attribute	Date_collection	time_precision	String	1970-01-01
attribute	Date_collection	units	String	unitless
variable	station		byte
attribute	station	_FillValue	byte	127
attribute	station	actual_range	byte	2, 11
attribute	station	bcodmo_name	String	station
attribute	station	description	String	station number
attribute	station	long_name	String	Station
attribute	station	units	String	unitless
variable	depth		double
attribute	depth	_CoordinateAxisType	String	Height
attribute	depth	_CoordinateZisPositive	String	down
attribute	depth	_FillValue	double	NaN
attribute	depth	actual_range	double	1.6, 55.5
attribute	depth	axis	String	Z
attribute	depth	bcodmo_name	String	depth
attribute	depth	colorBarMaximum	double	8000.0
attribute	depth	colorBarMinimum	double	-8000.0
attribute	depth	colorBarPalette	String	TopographyDepth
attribute	depth	description	String	depth of sample
attribute	depth	ioos_category	String	Location
attribute	depth	long_name	String	Depth
attribute	depth	nerc_identifier	String	https://vocab.nerc.ac.uk/collection/P09/current/DEPH/
attribute	depth	positive	String	down
attribute	depth	standard_name	String	depth
attribute	depth	units	String	m

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.