ERDDAP > info > bcodmo_dataset_665454

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
		data	graph		files	public	[BLASTp homology data] - BLASTp homology data from genes obtained in samples collected on the Gould (LMG1411) cruise in the Western Antarctica Peninsula during 2014 (Polar Transcriptomes project). (Iron and Light Limitation in Ecologically Important Polar Diatoms: Comparative Transcriptomics and Development of Molecular Indicators)		F   I   M	background			BCO-DMO	bcodmo_dataset_665454

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	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%. Illumina TruSeq adapters and poly-A tails were trimmed from raw reads using the Fastx_toolkit clipper function. Fastq_quality_filter was used to remove poor quality sequences, such that remaining sequences had a minimum quality score of 20 with a minimum of 80% of bases within a\u00a0read\u00a0meeting this quality score requirement. Any remaining raw sequences less than 50 base pairs in length were also removed. Merged files were assembled\u00a0de novo\u00a0using Trinity (Grabherr et al. 2011). The resulting assembly was filtered to remove contigs less than 200 bp in length. Trinity-assembled contigs which exhibited sequence overlap were grouped into isogroups which were then used for sequence homology searches (BLASTx E-value \u2264 10-4) against the Kyoto Encyclopedia of Genes and Genomes (KEGG) databases (Kanehisa 2006). Gene biogeographical distributions -\u00a020 genes of interest were selected in the study to investigate the molecular basis of iron and light limitation in polar diatoms. Reference sequences for each of these genes were obtained from the\u00a0F.\u00a0cylindrus\u00a0and\u00a0P.\u00a0tricornutum\u00a0JGI genome portals and\u00a0T.\u00a0pseudonana\u00a0and\u00a0T.\u00a0oceanica\u00a0NCBI and GenBank repositories. Reference sequences were identified in the transcriptomes by translated nucleotide homology searches (tBLASTn) with an e-value cutoff of <10-5. A reciprocal tBLASTn homology search was performed for each transcriptome against the KEGG GENES database, using the single- directional\u00a0best-hit\u00a0method in the KAAS online tool to ensure consistent gene annotations (Moriya et al. 2007). Subsequently, reference sequences were identified in the MMETSP protein database by BLASTp (e-value <10-5) homology searches among the diatom transcriptomes. The transcriptomes and their associated latitude and longitude were obtained from iMicrobe Data Commons (Project Code CAM_P_0001000) and the National Center for Marine Algae and Microbiota (NCMA). Custom Matlab scripts allowed global biogeographical distribution of key genes of interest to be mapped.
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	BLASTp Homology 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	2016-11-21T21:11:01Z
attribute	NC_GLOBAL	date_modified	String	2019-06-11T16:47:19Z
attribute	NC_GLOBAL	defaultDataQuery	String	&amp;time&lt;now
attribute	NC_GLOBAL	doi	String	10.1575/1912/bco-dmo.665454.1
attribute	NC_GLOBAL	Easternmost_Easting	double	163.0
attribute	NC_GLOBAL	geospatial_lat_max	double	77.8333
attribute	NC_GLOBAL	geospatial_lat_min	double	-77.8333
attribute	NC_GLOBAL	geospatial_lat_units	String	degrees_north
attribute	NC_GLOBAL	geospatial_lon_max	double	163.0
attribute	NC_GLOBAL	geospatial_lon_min	double	-159.4166667
attribute	NC_GLOBAL	geospatial_lon_units	String	degrees_east
attribute	NC_GLOBAL	infoUrl	String	https://www.bco-dmo.org/dataset/665454
attribute	NC_GLOBAL	institution	String	BCO-DMO
attribute	NC_GLOBAL	instruments_0_acronym	String	Inverted Microscope
attribute	NC_GLOBAL	instruments_0_dataset_instrument_description	String	Used to perform isolations
attribute	NC_GLOBAL	instruments_0_dataset_instrument_nid	String	665461
attribute	NC_GLOBAL	instruments_0_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_0_instrument_external_identifier	String	https://vocab.nerc.ac.uk/collection/L05/current/LAB05/
attribute	NC_GLOBAL	instruments_0_instrument_name	String	Inverted Microscope
attribute	NC_GLOBAL	instruments_0_instrument_nid	String	675
attribute	NC_GLOBAL	instruments_0_supplied_name	String	Olympus CKX41
attribute	NC_GLOBAL	instruments_1_acronym	String	Bioanalyzer
attribute	NC_GLOBAL	instruments_1_dataset_instrument_description	String	Used to determine RNA integrity
attribute	NC_GLOBAL	instruments_1_dataset_instrument_nid	String	665464
attribute	NC_GLOBAL	instruments_1_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_1_instrument_name	String	Bioanalyzer
attribute	NC_GLOBAL	instruments_1_instrument_nid	String	626182
attribute	NC_GLOBAL	instruments_1_supplied_name	String	Agilent Bioanalyzer 2100
attribute	NC_GLOBAL	keywords	String	bco, bco-dmo, biological, chemical, clade, data, dataset, dmo, e_value, erddap, gene, genus, latitude, longitude, management, mmetsp, MMETSP_ID, oceanography, office, preliminary, species, strain, subject, subject_ID, value
attribute	NC_GLOBAL	license	String	https://www.bco-dmo.org/dataset/665454/license
attribute	NC_GLOBAL	metadata_source	String	https://www.bco-dmo.org/api/dataset/665454
attribute	NC_GLOBAL	Northernmost_Northing	double	77.8333
attribute	NC_GLOBAL	param_mapping	String	{'665454': {'lat': 'master - latitude', 'lon': 'master - longitude'}}
attribute	NC_GLOBAL	parameter_source	String	https://www.bco-dmo.org/mapserver/dataset/665454/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	Southernmost_Northing	double	-77.8333
attribute	NC_GLOBAL	standard_name_vocabulary	String	CF Standard Name Table v55
attribute	NC_GLOBAL	summary	String	BLASTp homology data from genes obtained in samples collected on the Gould (LMG1411) cruise in the Western Antarctica Peninsula during 2014 (Polar Transcriptomes project).
attribute	NC_GLOBAL	title	String	[BLASTp homology data] - BLASTp homology data from genes obtained in samples collected on the Gould (LMG1411) cruise in the Western Antarctica Peninsula during 2014 (Polar Transcriptomes project). (Iron and Light Limitation in Ecologically Important Polar Diatoms: Comparative Transcriptomics and Development of Molecular Indicators)
attribute	NC_GLOBAL	version	String	1
attribute	NC_GLOBAL	Westernmost_Easting	double	-159.4166667
attribute	NC_GLOBAL	xml_source	String	osprey2erddap.update_xml() v1.3
variable	gene		String
attribute	gene	bcodmo_name	String	unknown
attribute	gene	description	String	Gene analyzed
attribute	gene	long_name	String	Gene
attribute	gene	units	String	unitless
variable	genus		String
attribute	genus	bcodmo_name	String	genus
attribute	genus	description	String	Genus analyzed
attribute	genus	long_name	String	Genus
attribute	genus	units	String	unitless
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	strain		String
attribute	strain	bcodmo_name	String	unknown
attribute	strain	description	String	Strain ID
attribute	strain	long_name	String	Strain
attribute	strain	units	String	unitless
variable	MMETSP_ID		String
attribute	MMETSP_ID	bcodmo_name	String	unknown
attribute	MMETSP_ID	description	String	MMETSP ID
attribute	MMETSP_ID	long_name	String	MMETSP ID
attribute	MMETSP_ID	units	String	unitless
variable	subject_ID		String
attribute	subject_ID	bcodmo_name	String	sample
attribute	subject_ID	description	String	Strain ID
attribute	subject_ID	long_name	String	Subject ID
attribute	subject_ID	nerc_identifier	String	https://vocab.nerc.ac.uk/collection/P02/current/ACYC/
attribute	subject_ID	units	String	unitless
variable	e_value		double
attribute	e_value	_FillValue	double	NaN
attribute	e_value	actual_range	double	0.0, 5.0E-6
attribute	e_value	bcodmo_name	String	unknown
attribute	e_value	description	String	E-value
attribute	e_value	long_name	String	E Value
attribute	e_value	units	String	unitless
variable	latitude		double
attribute	latitude	_CoordinateAxisType	String	Lat
attribute	latitude	_FillValue	double	NaN
attribute	latitude	actual_range	double	-77.8333, 77.8333
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; N 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	-159.4166667, 163.0
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; E 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	standard_name	String	longitude
attribute	longitude	units	String	degrees_east
variable	clade		String
attribute	clade	bcodmo_name	String	unknown
attribute	clade	description	String	Clade category
attribute	clade	long_name	String	Clade
attribute	clade	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.