ERDDAP > info > bcodmo_dataset_652259

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	[IrnBru MV1405 - Bacteria and Virus Abundance] - Bacteria and virus abundance data collected from the R/V Melville MV1405 along the California coastline during 2014 (Linking physiological and molecular aspects of diatom silicification in field populations)		F   I   M	background			BCO-DMO	bcodmo_dataset_652259

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,.odvTxt
attribute	NC_GLOBAL	acquisition_description	String	Environmental Sample Collection 1. Transfer 1 ml of whole seawater to a 2 ml cryovial. 2. Add 20 ul of 25% glutaraldehyde for a final concentration of 0.5%. 3. Incubate at 4 degrees celsius for 30 min. 4. Flash freeze in liquid N2\u00a0and store at -80 degrees celsius. Fluorescent DNA staining (for bacterial and viral abundances) 1. Thaw samples. 2. To 20 ul of sample, add 980 ul 1X TE buffer with SYBR Gold (see recipe below)\u00a0 3. Heat to 80 degrees celsius for 10 min in the dark 4. Cool at RT for 5 min 5. Analyze via flow cytometry Analysis (for bacterial and viral abundances) Samples are analyzed on Influx Model 209S Mariner flow cytometer using BD Software (BD Biosciences). 1. An initial Forward Scatter (FSC) vs Side Scatter (SSC) configuration is determined using Molecular Probes Flow Cytometry Sub-micron particles size reference kit (Cat#F13839) consisting of 0.02, 0.1, 0.5, 1.0 and 2.0 um fluorescent beads. 2. A gating hierarchy is established using both beads and previously determined virus and bacteria populations as\u00a0reference\u00a0(Sybr Gold Fluorescence versus SSC cytogram). 3. Samples are analyzed using a 488 nm laser for excitation and a minimum trigger threshold is established using 542/15 nm (SYBR Gold) emission. TE buffer with SYBR Gold recipe 1X TE (for 100\u00a0mls) 1 ml of 1M Tris, pH 8.0 1 ml of 0.5 mM EDTA 98\u00a0mls\u00a0MQ water Store 4 degrees celsius 1X TE + SYBR Gold (for 10\u00a0mls) 1. Filter 10\u00a0mls\u00a01 TE buffer, 0.22 um filter 2. 1:20,0000 dilution of SYBR Gold stock (Molecular Probes) (0.5 ul stock to 10\u00a0mls\u00a0TE buffer)\u00a0
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	awards_1_award_nid	String	558203
attribute	NC_GLOBAL	awards_1_award_number	String	OCE-1334387
attribute	NC_GLOBAL	awards_1_data_url	String	http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1334387
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	cdm_data_type	String	Other
attribute	NC_GLOBAL	comment	String	Bacteria and Virus Abundance K. Thamatrakoln and M. Brzezinski, PIs Version 20 July 2016
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	2016-07-20T20:46:58Z
attribute	NC_GLOBAL	date_modified	String	2019-06-06T15:37:18Z
attribute	NC_GLOBAL	defaultDataQuery	String	&time<now
attribute	NC_GLOBAL	doi	String	10.1575/1912/bco-dmo.652259.1
attribute	NC_GLOBAL	Easternmost_Easting	double	-120.02587
attribute	NC_GLOBAL	geospatial_lat_max	double	42.6495
attribute	NC_GLOBAL	geospatial_lat_min	double	34.23125
attribute	NC_GLOBAL	geospatial_lat_units	String	degrees_north
attribute	NC_GLOBAL	geospatial_lon_max	double	-120.02587
attribute	NC_GLOBAL	geospatial_lon_min	double	-126.6157
attribute	NC_GLOBAL	geospatial_lon_units	String	degrees_east
attribute	NC_GLOBAL	geospatial_vertical_max	double	60.0
attribute	NC_GLOBAL	geospatial_vertical_min	double	2.0
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/652259
attribute	NC_GLOBAL	institution	String	BCO-DMO
attribute	NC_GLOBAL	instruments_0_acronym	String	Flow Cytometer
attribute	NC_GLOBAL	instruments_0_dataset_instrument_description	String	Samples analyzed on flow cytometer using BD Software (BD Biosciences).
attribute	NC_GLOBAL	instruments_0_dataset_instrument_nid	String	652268
attribute	NC_GLOBAL	instruments_0_description	String	Flow cytometers (FC or FCM) are automated instruments that quantitate properties of single cells, one cell at a time. They can measure cell size, cell granularity, the amounts of cell components such as total DNA, newly synthesized DNA, gene expression as the amount messenger RNA for a particular gene, amounts of specific surface receptors, amounts of intracellular proteins, or transient signalling events in living cells. (from: http://www.bio.umass.edu/micro/immunology/facs542/facswhat.htm)
attribute	NC_GLOBAL	instruments_0_instrument_external_identifier	String	https://vocab.nerc.ac.uk/collection/L05/current/LAB37/
attribute	NC_GLOBAL	instruments_0_instrument_name	String	Flow Cytometer
attribute	NC_GLOBAL	instruments_0_instrument_nid	String	660
attribute	NC_GLOBAL	instruments_0_supplied_name	String	Influx Model 209S Mariner Flow Cytometer
attribute	NC_GLOBAL	keywords	String	bacteria, bco, bco-dmo, biological, chemical, conductivity, cruise, cruise_id, ctd, data, dataset, date, date_GMT, depth, dmo, erddap, iso, latitude, longitude, management, oceanography, office, preliminary, sonde, station, temperature, time, time_GMT, virus, yearday, yearday_GMT
attribute	NC_GLOBAL	license	String	https://www.bco-dmo.org/dataset/652259/license
attribute	NC_GLOBAL	metadata_source	String	https://www.bco-dmo.org/api/dataset/652259
attribute	NC_GLOBAL	Northernmost_Northing	double	42.6495
attribute	NC_GLOBAL	param_mapping	String	{'652259': {'lat': 'master - latitude', 'depth': 'flag - depth', 'lon': 'master - longitude', 'ISO_DateTime_UTC': 'flag - time'}}
attribute	NC_GLOBAL	parameter_source	String	https://www.bco-dmo.org/mapserver/dataset/652259/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	University of California-Santa Barbara
attribute	NC_GLOBAL	people_1_affiliation_acronym	String	UCSB-LifeSci
attribute	NC_GLOBAL	people_1_person_name	String	Mark A. Brzezinski
attribute	NC_GLOBAL	people_1_person_nid	String	50663
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	Rutgers University
attribute	NC_GLOBAL	people_2_affiliation_acronym	String	Rutgers IMCS
attribute	NC_GLOBAL	people_2_person_name	String	Kimberlee Thamatrakoln
attribute	NC_GLOBAL	people_2_person_nid	String	558200
attribute	NC_GLOBAL	people_2_role	String	Contact
attribute	NC_GLOBAL	people_2_role_type	String	related
attribute	NC_GLOBAL	people_3_affiliation	String	Woods Hole Oceanographic Institution
attribute	NC_GLOBAL	people_3_affiliation_acronym	String	WHOI BCO-DMO
attribute	NC_GLOBAL	people_3_person_name	String	Hannah Ake
attribute	NC_GLOBAL	people_3_person_nid	String	650173
attribute	NC_GLOBAL	people_3_role	String	BCO-DMO Data Manager
attribute	NC_GLOBAL	people_3_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	34.23125
attribute	NC_GLOBAL	standard_name_vocabulary	String	CF Standard Name Table v55
attribute	NC_GLOBAL	subsetVariables	String	cruise_id
attribute	NC_GLOBAL	summary	String	Bacteria and virus abundance data collected from the R/V Melville MV1405 along the California coastline during 2014
attribute	NC_GLOBAL	time_coverage_end	String	2014-07-24T19:20:00Z
attribute	NC_GLOBAL	time_coverage_start	String	2014-07-04T16:20:00Z
attribute	NC_GLOBAL	title	String	[IrnBru MV1405 - Bacteria and Virus Abundance] - Bacteria and virus abundance data collected from the R/V Melville MV1405 along the California coastline during 2014 (Linking physiological and molecular aspects of diatom silicification in field populations)
attribute	NC_GLOBAL	version	String	1
attribute	NC_GLOBAL	Westernmost_Easting	double	-126.6157
attribute	NC_GLOBAL	xml_source	String	osprey2erddap.update_xml() v1.3
variable	cruise_id		String
attribute	cruise_id	bcodmo_name	String	cruise_id
attribute	cruise_id	description	String	cruise where samples were collected
attribute	cruise_id	long_name	String	Cruise Id
attribute	cruise_id	units	String	unitless
variable	CTD		byte
attribute	CTD	_FillValue	byte	127
attribute	CTD	actual_range	byte	1, 29
attribute	CTD	bcodmo_name	String	cast
attribute	CTD	description	String	CTD cast
attribute	CTD	long_name	String	CTD
attribute	CTD	units	String	unitless
variable	station		byte
attribute	station	_FillValue	byte	127
attribute	station	actual_range	byte	1, 29
attribute	station	bcodmo_name	String	station
attribute	station	description	String	station where samples were collected
attribute	station	long_name	String	Station
attribute	station	units	String	unitless
variable	date_GMT		String
attribute	date_GMT	bcodmo_name	String	date_gmt
attribute	date_GMT	description	String	GMT date of cast; mm/dd/yy
attribute	date_GMT	long_name	String	Date GMT
attribute	date_GMT	units	String	unitless
variable	time_GMT		String
attribute	time_GMT	bcodmo_name	String	time_gmt
attribute	time_GMT	description	String	GMT time of cast; HH:MM
attribute	time_GMT	long_name	String	Time GMT
attribute	time_GMT	units	String	unitless
variable	yearday_GMT		short
attribute	yearday_GMT	_FillValue	short	32767
attribute	yearday_GMT	actual_range	short	185, 205
attribute	yearday_GMT	bcodmo_name	String	yrday
attribute	yearday_GMT	description	String	GMT day of year.
attribute	yearday_GMT	long_name	String	Yearday GMT
attribute	yearday_GMT	units	String	unitless
variable	latitude		double
attribute	latitude	_CoordinateAxisType	String	Lat
attribute	latitude	_FillValue	double	NaN
attribute	latitude	actual_range	double	34.23125, 42.6495
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
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	-126.6157, -120.02587
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
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	depth		double
attribute	depth	_CoordinateAxisType	String	Height
attribute	depth	_CoordinateZisPositive	String	down
attribute	depth	_FillValue	double	NaN
attribute	depth	actual_range	double	2.0, 60.0
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 collection
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
variable	bacteria		float
attribute	bacteria	_FillValue	float	NaN
attribute	bacteria	actual_range	float	1680000.0, 4260000.0
attribute	bacteria	bcodmo_name	String	abundance
attribute	bacteria	description	String	bacteria-like particle abundance
attribute	bacteria	long_name	String	Bacteria
attribute	bacteria	nerc_identifier	String	https://vocab.nerc.ac.uk/collection/P03/current/B070/
attribute	bacteria	units	String	bacteria per milliliter
variable	virus		float
attribute	virus	_FillValue	float	NaN
attribute	virus	actual_range	float	6880000.0, 2.8E7
attribute	virus	bcodmo_name	String	abundance
attribute	virus	description	String	virus-like particle abundance (VLP)
attribute	virus	long_name	String	Virus
attribute	virus	nerc_identifier	String	https://vocab.nerc.ac.uk/collection/P03/current/B070/
attribute	virus	units	String	VLP per milliliter
variable	time		double
attribute	time	_CoordinateAxisType	String	Time
attribute	time	actual_range	double	1.4044908E9, 1.4062296E9
attribute	time	axis	String	T
attribute	time	bcodmo_name	String	ISO_DateTime_UTC
attribute	time	description	String	DateTime (UTC) ISO formatted
attribute	time	ioos_category	String	Time
attribute	time	long_name	String	ISO Date Time UTC
attribute	time	nerc_identifier	String	https://vocab.nerc.ac.uk/collection/P01/current/DTUT8601/
attribute	time	source_name	String	ISO_DateTime_UTC
attribute	time	standard_name	String	time
attribute	time	time_origin	String	01-JAN-1970 00:00:00
attribute	time	time_precision	String	1970-01-01T00:00:00Z
attribute	time	units	String	seconds since 1970-01-01T00:00:00Z

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.