ERDDAP > info > bcodmo_dataset_666201

Grid DAP Data	Sub- set	Table DAP Data	Make A Graph	W M S	Source Data Files	Acces- sible	Title	Sum- mary	ISO, Metadata	Back- ground Info	RSS	E mail	Institution	Dataset ID
		data	graph		files	public	Diatom growth rates from samples collected on the Gould cruise LMG1411 in the Western Antarctica Peninsula from 2014 (Polar Transcriptomes project)		I   M	background			BCO-DMO	bcodmo_dataset_666201

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
attribute	NC_GLOBAL	acquisition_description	String	Nine species of diatoms were isolated from the Western Antarctic Peninsula along the PalmerLTER sampling grid in 2013 and 2014. Isolations were performed using an Olympus CKX41 inverted microscope by single cell isolation with a micropipette (Anderson 2005). Diatom species were identified by morphological characterization and 18S rRNA gene (rDNA) sequencing. DNA was extracted with the DNeasy Plant Mini Kit according to the manufacturer\u2019s protocols (Qiagen). Amplification of the nuclear 18S rDNA region was achieved with standard PCR protocols using eukaryotic-specific, universal 18S forward and reverse primers. Primer sequences were obtained from Medlin et al. (1982). The length of the region amplified is approximately 1800 base pairs (bp ).\u00a0Pseudo-nitzschia\u00a0species are often difficult to identify by their 18S rDNA sequence, therefore, additional support of the taxonomic identification of\u00a0P.\u00a0subcurvata\u00a0was provided through sequencing of the 18S-ITS1-5.8S regions. Amplification of this region was performed with the 18SF-euk and 5.8SR_euk primers of Hubbard et al. (2008). PCR products were purified using either QIAquick PCR Purification Kit (Qiagen) or ExoSAP-IT (Affymetrix) and sequenced by Sanger DNA sequencing (Genewiz). Sequences were edited using Geneious Pro software ([http://www.geneious.com](\\"http://www.geneious.com\\"), Kearse et al., 2012) and BLASTn sequence homology searches were performed against the NCBI nucleotide non-redundant (nr) database to determine species with a cutoff identity of 98%. Diatom phylogenetic analysis was performed with Geneious Pro and included 71 additional diatom 18S rDNA sequences from publically available genomes and transcriptomes, including those in the MMETSP database. Diatom sequences were trimmed to the same length and aligned with MUSCLE (Edgar 2004). A phylogenetic tree was created in Mega with the Maximum-likelihood method of tree reconstruction, the Jukes-Cantor genetic distance model (Jukes and Cantor 1969), and 100 bootstrap replicates. Isolates were maintained at 4 deg C in constant irradiance at intensities of either 10\u00a0umol\u00a0photons m-2\u00a0s-1\u00a0(low light) or 90\u00a0umol\u00a0photons m-2\u00a0s-1\u00a0(growth saturating light) and with media containing high and low iron concentrations. Cultures were grown in the synthetic seawater medium, AQUIL, enriched with filter sterilized vitamin and trace metal ion buffer containing 100\u00a0umol\u00a0L-1\u00a0EDTA. The growth media also contained 300 \u03bcmol L-1\u00a0nitrate, 200\u00a0umol\u00a0L-1\u00a0silicic acid and 20\u00a0umol\u00a0L-1\u00a0phosphate. Premixed Fe-EDTA (1:1) was added separately for total iron concentrations of either 1370 nmol L-1\u00a0or 3.1 nmol L-1. Cultures were grown in acid-washed 28 mL polycarbonate centrifuge tubes (Nalgene) and maintained in exponential phase by dilution. Specific growth rates of successive transfers were calculated from the linear regression of the natural\u00a0log of\u00a0in vivo\u00a0chlorophyll\u00a0a\u00a0fluorescence using a Turner 10-AU fluorometer (Brand et al. 1981).\u00a0 Statistical analyses of growth rates and photophysiological data were performed with SigmaPlot 12.5 (SysStat Software Inc.). To test for significant differences between treatments, Two-Way Analysis of Variance (ANOVA) was performed with a significance level set\u00a0to\u00a0p<0.05. ANOVA also tests for normality using Shapiro-Wilks and Equal Variance tests. Because ANOVA does not test all interactions, an unpaired t-test was performed between \u2013FeLL and +FeSL for u, Fv:Fm, and \u00a0oPSII. All tests passed the Shapiro-Wilks Normality tests unless otherwise stated, in which case\u00a0p-values are representative of the Mann-Whitney Rank Sum test. Post-hoc Tukey tests were also performed in order to determine which treatments differed significantly (p\u00a0< 0.05). Cultures for high throughput sequencing of mRNA were grown in acid-washed 2L polycarbonate bottles in iron-replete conditions under growth-saturating light (90\u00a0umol\u00a0photons m-2\u00a0s-1). After reaching late exponential/early stationary phase, cultures were harvested onto polycarbonate filters (3.0 um pore size, 25 mm) and stored at -80 deg C. Total RNA was extracted using the RNAqueous 4PCR Kit (Ambion) according to the manufacturer\u2019s protocols. Residual genomic DNA was eliminated by DNAseI digestion at 37 deg C for 45 min. An Agilent Bioanalyzer 2100 was used to determine RNA integrity. mRNA libraries were generated with ~2\u00a0ug\u00a0of total RNA and prepared with the Illumina TruSeq Stranded mRNA Library Preparation Kit. Samples were individually barcoded and pooled prior to sequencing on the Illumina MiSeq platform at the High Throughput Sequencing Facility (HTSF) at UNC-Chapel Hill. Sequencing resulted in approximately 0.7-2 million paired-end reads of 2x300bp per sample.\u200b
attribute	NC_GLOBAL	awards_0_award_nid	String	653228
attribute	NC_GLOBAL	awards_0_award_number	String	PLR-1341479
attribute	NC_GLOBAL	awards_0_data_url	String	http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1341479
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	Dr Chris H. Fritsen
attribute	NC_GLOBAL	awards_0_program_manager_nid	String	50502
attribute	NC_GLOBAL	cdm_data_type	String	Other
attribute	NC_GLOBAL	comment	String	Growth Rate Data Adrian Marchetti, PI Version 11 October 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	2016-11-28T17:33:50Z
attribute	NC_GLOBAL	date_modified	String	2019-04-17T20:12:02Z
attribute	NC_GLOBAL	defaultDataQuery	String	&amp;time&lt;now
attribute	NC_GLOBAL	doi	String	10.1575/1912/bco-dmo.666201.1
attribute	NC_GLOBAL	infoUrl	String	https://www.bco-dmo.org/dataset/666201
attribute	NC_GLOBAL	institution	String	BCO-DMO
attribute	NC_GLOBAL	instruments_0_acronym	String	Fluorometer
attribute	NC_GLOBAL	instruments_0_dataset_instrument_description	String	Used to determine cell growth rates
attribute	NC_GLOBAL	instruments_0_dataset_instrument_nid	String	666209
attribute	NC_GLOBAL	instruments_0_description	String	A fluorometer or fluorimeter is a device used to measure parameters of fluorescence: its intensity and wavelength distribution of emission spectrum after excitation by a certain spectrum of light. The instrument is designed to measure the amount of stimulated electromagnetic radiation produced by pulses of electromagnetic radiation emitted into a water sample or in situ.
attribute	NC_GLOBAL	instruments_0_instrument_external_identifier	String	https://vocab.nerc.ac.uk/collection/L05/current/113/
attribute	NC_GLOBAL	instruments_0_instrument_name	String	Fluorometer
attribute	NC_GLOBAL	instruments_0_instrument_nid	String	484
attribute	NC_GLOBAL	instruments_0_supplied_name	String	Turner 10-AU
attribute	NC_GLOBAL	instruments_1_acronym	String	Inverted Microscope
attribute	NC_GLOBAL	instruments_1_dataset_instrument_description	String	Used to perform isolations
attribute	NC_GLOBAL	instruments_1_dataset_instrument_nid	String	666208
attribute	NC_GLOBAL	instruments_1_description	String	An inverted microscope is a microscope with its light source and condenser on the top, above the stage pointing down, while the objectives and turret are below the stage pointing up. It was invented in 1850 by J. Lawrence Smith, a faculty member of Tulane University (then named the Medical College of Louisiana). Inverted microscopes are useful for observing living cells or organisms at the bottom of a large container (e.g. a tissue culture flask) under more natural conditions than on a glass slide, as is the case with a conventional microscope. Inverted microscopes are also used in micromanipulation applications where space above the specimen is required for manipulator mechanisms and the microtools they hold, and in metallurgical applications where polished samples can be placed on top of the stage and viewed from underneath using reflecting objectives. The stage on an inverted microscope is usually fixed, and focus is adjusted by moving the objective lens along a vertical axis to bring it closer to or further from the specimen. The focus mechanism typically has a dual concentric knob for coarse and fine adjustment. Depending on the size of the microscope, four to six objective lenses of different magnifications may be fitted to a rotating turret known as a nosepiece. These microscopes may also be fitted with accessories for fitting still and video cameras, fluorescence illumination, confocal scanning and many other applications.
attribute	NC_GLOBAL	instruments_1_instrument_external_identifier	String	https://vocab.nerc.ac.uk/collection/L05/current/LAB05/
attribute	NC_GLOBAL	instruments_1_instrument_name	String	Inverted Microscope
attribute	NC_GLOBAL	instruments_1_instrument_nid	String	675
attribute	NC_GLOBAL	instruments_1_supplied_name	String	Olympus CKX41
attribute	NC_GLOBAL	instruments_2_acronym	String	Bioanalyzer
attribute	NC_GLOBAL	instruments_2_dataset_instrument_description	String	Used to determine RNA integrity
attribute	NC_GLOBAL	instruments_2_dataset_instrument_nid	String	666211
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 Bioanalyzer 2100
attribute	NC_GLOBAL	keywords	String	bco, bco-dmo, biological, chemical, data, dataset, depth, dmo, erddap, error, management, mean, mean_FvFm, mean_sigma, mean_specific_u, oceanography, office, preliminary, profiler, propogation, propogation_error_FvFm, propogation_error_sigma, propogation_error_u, relative, relative_FvFm, relative_sigma, relative_u, salinity, salinity-temperature-depth, sample, sample_size_FvFm, sample_size_sigma, sample_size_u, sigma, size, species, specific, std, std_error_FvFm, std_error_sigma, std_error_u, temperature, treatment, u
attribute	NC_GLOBAL	license	String	https://www.bco-dmo.org/dataset/666201/license
attribute	NC_GLOBAL	metadata_source	String	https://www.bco-dmo.org/api/dataset/666201
attribute	NC_GLOBAL	param_mapping	String	{'666201': {}}
attribute	NC_GLOBAL	parameter_source	String	https://www.bco-dmo.org/mapserver/dataset/666201/parameters
attribute	NC_GLOBAL	people_0_affiliation	String	University of North Carolina at Chapel Hill
attribute	NC_GLOBAL	people_0_affiliation_acronym	String	UNC-Chapel Hill
attribute	NC_GLOBAL	people_0_person_name	String	Adrian Marchetti
attribute	NC_GLOBAL	people_0_person_nid	String	527120
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 North Carolina at Chapel Hill
attribute	NC_GLOBAL	people_1_affiliation_acronym	String	UNC-Chapel Hill
attribute	NC_GLOBAL	people_1_person_name	String	Adrian Marchetti
attribute	NC_GLOBAL	people_1_person_nid	String	527120
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	Hannah Ake
attribute	NC_GLOBAL	people_2_person_nid	String	650173
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	Polar_Transcriptomes
attribute	NC_GLOBAL	projects_0_acronym	String	Polar_Transcriptomes
attribute	NC_GLOBAL	projects_0_description	String	The Southern Ocean surrounding Antarctica is changing rapidly in response to Earth's warming climate. These changes will undoubtedly influence communities of primary producers (the organisms at the base of the food chain, particularly plant-like organisms using sunlight for energy) by altering conditions that influence their growth and composition. Because primary producers such as phytoplankton play an important role in global biogeochemical cycling, it is essential to understand how they will respond to changes in their environment. The growth of phytoplankton in certain regions of the Southern Ocean is constrained by steep gradients in chemical and physical properties that vary in both space and time. Light and iron have been identified as key variables influencing phytoplankton abundance and distribution within Antarctic waters. Microscopic algae known as diatoms are dominant members of the phytoplankton and sea ice communities, accounting for significant proportions of primary production. The overall objective of this project is to identify the molecular bases for the physiological responses of polar diatoms to varying light and iron conditions. The project should provide a means of evaluating the extent these factors regulate diatom growth and influence net community productivity in Antarctic waters. The project will also further the NSF goals of making scientific discoveries available to the general public and of training new generations of scientists. It will facilitate the teaching and learning of polar-related topics by translating the research objectives into readily accessible educational materials for middle-school students. This project will also provide funding to enable a graduate student and several undergraduate students to be trained in the techniques and perspectives of modern biology. Although numerous studies have investigated how polar diatoms are affected by varying light and iron, the cellular mechanisms leading to their distinct physiological responses remain unknown. Using comparative transcriptomics, the expression patterns of key genes and metabolic pathways in several ecologically important polar diatoms recently isolated from Antarctic waters and grown under varying iron and irradiance conditions will be examined. In addition, molecular indicators for iron and light limitation will be developed within these polar diatoms through the identification of iron- and light-responsive genes -- the expression patterns of which can be used to determine their physiological status. Upon verification in laboratory cultures, these indicators will be utilized by way of metatranscriptomic sequencing to examine iron and light limitation in natural diatom assemblages collected along environmental gradients in Western Antarctic Peninsula waters. In order to fully understand the role phytoplankton play in Southern Ocean biogeochemical cycles, dependable methods that provide a means of elucidating the physiological status of phytoplankton at any given time and location are essential.
attribute	NC_GLOBAL	projects_0_end_date	String	2017-07
attribute	NC_GLOBAL	projects_0_geolocation	String	Antarctica
attribute	NC_GLOBAL	projects_0_name	String	Iron and Light Limitation in Ecologically Important Polar Diatoms: Comparative Transcriptomics and Development of Molecular Indicators
attribute	NC_GLOBAL	projects_0_project_nid	String	653229
attribute	NC_GLOBAL	projects_0_project_website	String	http://www.nsf.gov/awardsearch/showAward?AWD_ID=1341479
attribute	NC_GLOBAL	projects_0_start_date	String	2014-08
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	standard_name_vocabulary	String	CF Standard Name Table v55
attribute	NC_GLOBAL	summary	String	Diatom growth rates from samples collected on the Gould cruise LMG1411 in the Western Antarctica Peninsula from 2014 (Polar Transcriptomes project)
attribute	NC_GLOBAL	title	String	Diatom growth rates from samples collected on the Gould cruise LMG1411 in the Western Antarctica Peninsula from 2014 (Polar Transcriptomes project)
attribute	NC_GLOBAL	version	String	1
attribute	NC_GLOBAL	xml_source	String	osprey2erddap.update_xml() v1.3
variable	species		String
attribute	species	bcodmo_name	String	species
attribute	species	description	String	Species analyzed
attribute	species	long_name	String	Species
attribute	species	units	String	unitless
variable	treatment		String
attribute	treatment	bcodmo_name	String	treatment
attribute	treatment	description	String	Treatment condition
attribute	treatment	long_name	String	Treatment
attribute	treatment	units	String	unitless
variable	mean_specific_u		String
attribute	mean_specific_u	bcodmo_name	String	mean
attribute	mean_specific_u	description	String	Average growth rate in a specific treatment
attribute	mean_specific_u	long_name	String	Mean Specific U
attribute	mean_specific_u	units	String	d -1
variable	relative_u		float
attribute	relative_u	_FillValue	float	NaN
attribute	relative_u	actual_range	float	0.36, 1.0
attribute	relative_u	bcodmo_name	String	growth
attribute	relative_u	description	String	Relative growth rate
attribute	relative_u	long_name	String	Relative U
attribute	relative_u	units	String	unitless
variable	std_error_u		float
attribute	std_error_u	_FillValue	float	NaN
attribute	std_error_u	actual_range	float	0.003, 0.058
attribute	std_error_u	bcodmo_name	String	standard error
attribute	std_error_u	colorBarMaximum	double	50.0
attribute	std_error_u	colorBarMinimum	double	0.0
attribute	std_error_u	description	String	Standard error of relative growth rate
attribute	std_error_u	long_name	String	Std Error U
attribute	std_error_u	units	String	unitless
variable	propogation_error_u		float
attribute	propogation_error_u	_FillValue	float	NaN
attribute	propogation_error_u	actual_range	float	0.01, 0.187
attribute	propogation_error_u	bcodmo_name	String	growth
attribute	propogation_error_u	colorBarMaximum	double	50.0
attribute	propogation_error_u	colorBarMinimum	double	0.0
attribute	propogation_error_u	description	String	Relative growth rate error
attribute	propogation_error_u	long_name	String	Propogation Error U
attribute	propogation_error_u	units	String	unitless
variable	sample_size_u		byte
attribute	sample_size_u	_FillValue	byte	127
attribute	sample_size_u	actual_range	byte	1, 14
attribute	sample_size_u	bcodmo_name	String	number
attribute	sample_size_u	description	String	Number of samples recorded
attribute	sample_size_u	long_name	String	Sample Size U
attribute	sample_size_u	units	String	unitless
variable	mean_FvFm		float
attribute	mean_FvFm	_FillValue	float	NaN
attribute	mean_FvFm	actual_range	float	0.25, 0.622
attribute	mean_FvFm	bcodmo_name	String	mean
attribute	mean_FvFm	description	String	Average photosynthetic efficiency
attribute	mean_FvFm	long_name	String	Mean Fv Fm
attribute	mean_FvFm	units	String	unitless
variable	relative_FvFm		float
attribute	relative_FvFm	_FillValue	float	NaN
attribute	relative_FvFm	actual_range	float	0.0, 1.251
attribute	relative_FvFm	bcodmo_name	String	Fv2Fm
attribute	relative_FvFm	description	String	Relative photosynthetic efficiency
attribute	relative_FvFm	long_name	String	Relative Fv Fm
attribute	relative_FvFm	units	String	unitless
variable	std_error_FvFm		float
attribute	std_error_FvFm	_FillValue	float	NaN
attribute	std_error_FvFm	actual_range	float	0.01, 0.071
attribute	std_error_FvFm	bcodmo_name	String	standard error
attribute	std_error_FvFm	colorBarMaximum	double	50.0
attribute	std_error_FvFm	colorBarMinimum	double	0.0
attribute	std_error_FvFm	description	String	Relative photosynthetic efficiency standard error
attribute	std_error_FvFm	long_name	String	Std Error Fv Fm
attribute	std_error_FvFm	units	String	unitless
variable	propogation_error_FvFm		float
attribute	propogation_error_FvFm	_FillValue	float	NaN
attribute	propogation_error_FvFm	actual_range	float	0.0, 0.144
attribute	propogation_error_FvFm	bcodmo_name	String	Fv2Fm
attribute	propogation_error_FvFm	colorBarMaximum	double	50.0
attribute	propogation_error_FvFm	colorBarMinimum	double	0.0
attribute	propogation_error_FvFm	description	String	Relative photosynthetic efficiency error
attribute	propogation_error_FvFm	long_name	String	Propogation Error Fv Fm
attribute	propogation_error_FvFm	units	String	unitless
variable	sample_size_FvFm		byte
attribute	sample_size_FvFm	_FillValue	byte	127
attribute	sample_size_FvFm	actual_range	byte	1, 12
attribute	sample_size_FvFm	bcodmo_name	String	Fv2Fm
attribute	sample_size_FvFm	description	String	Relative photosynthetic efficiency number of samples recorded
attribute	sample_size_FvFm	long_name	String	Sample Size Fv Fm
attribute	sample_size_FvFm	units	String	unitless
variable	mean_sigma		String
attribute	mean_sigma	bcodmo_name	String	mean
attribute	mean_sigma	description	String	Average functional absorption cross-section of PSII
attribute	mean_sigma	long_name	String	Mean Sigma
attribute	mean_sigma	units	String	A2 quanta -1
variable	relative_sigma		float
attribute	relative_sigma	_FillValue	float	NaN
attribute	relative_sigma	actual_range	float	0.752, 2.0
attribute	relative_sigma	bcodmo_name	String	unknown
attribute	relative_sigma	description	String	Relative function absorption cross-section of PSII
attribute	relative_sigma	long_name	String	Relative Sigma
attribute	relative_sigma	units	String	unitless
variable	std_error_sigma		float
attribute	std_error_sigma	_FillValue	float	NaN
attribute	std_error_sigma	actual_range	float	3.0, 48.0
attribute	std_error_sigma	bcodmo_name	String	standard error
attribute	std_error_sigma	colorBarMaximum	double	50.0
attribute	std_error_sigma	colorBarMinimum	double	0.0
attribute	std_error_sigma	description	String	Functional absorption cross-section of PSII standard error
attribute	std_error_sigma	long_name	String	Std Error Sigma
attribute	std_error_sigma	units	String	unitless
variable	propogation_error_sigma		float
attribute	propogation_error_sigma	_FillValue	float	NaN
attribute	propogation_error_sigma	actual_range	float	0.0, 0.207
attribute	propogation_error_sigma	bcodmo_name	String	unknown
attribute	propogation_error_sigma	colorBarMaximum	double	50.0
attribute	propogation_error_sigma	colorBarMinimum	double	0.0
attribute	propogation_error_sigma	description	String	Functional absorption cross-section of PSII error
attribute	propogation_error_sigma	long_name	String	Propogation Error Sigma
attribute	propogation_error_sigma	units	String	unitless
variable	sample_size_sigma		byte
attribute	sample_size_sigma	_FillValue	byte	127
attribute	sample_size_sigma	actual_range	byte	1, 12
attribute	sample_size_sigma	bcodmo_name	String	number
attribute	sample_size_sigma	description	String	Functional absorption cross-section of PSII number of samples recorded
attribute	sample_size_sigma	long_name	String	Sample Size Sigma
attribute	sample_size_sigma	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.