ERDDAP > info > bcodmo_dataset_665427

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	[MMETSP locations and e-values] - Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP) location information on samples obtained on Gould (LMG1411) 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_665427

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%. 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. 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). BUSCO (Benchmarking Universal Single-Copy Orthologs) was used to assess the completeness of genomes and transcriptomes based on sets of\u00a0single copy\u00a0orthologous groups derived from OrthoDB that are highly conserved within multiple lineages (Felipe et al. 2015). Completed, duplicated and fragmented orthologs were determined by meeting an \u2018expected score\u2019 and having aligned sequences within two standard deviations of the BUSCO gene\u2019s length.\u00a0A second\u00a0metric of completeness was performed by evaluating conserved pathways, such as the ribosome and spliceosome, using the single-directional\u00a0best-hit\u00a0method in the KEGG Automatic Annotation Server (KAAS) (Moriya et al. 2007).\u00a0Finally\u00a0contiguity,\u00a0was calculated at the 0.75 level as according to Martin and Wang (2011) with custom scripts. For each transcriptome, unassembled sequence reads were aligned to the final Trinity assembly using Bowtie 2 (Langmead 2012). Mapped reads were normalized by the Reads per Kilobase per Million reads method (RPKM) (Mortazavi et al. 2008). 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	MMETSP Location 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	2016-11-21T20:24:33Z
attribute	NC_GLOBAL	date_modified	String	2019-04-17T20:24:03Z
attribute	NC_GLOBAL	defaultDataQuery	String	&amp;time&lt;now
attribute	NC_GLOBAL	doi	String	10.1575/1912/bco-dmo.665427.1
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/665427
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	665434
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	665437
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, data, dataset, dmo, erddap, evalue, evalue_mean, evalue_paste, genus, genus_max, lat2, latitude, lon_360, longitude, management, max, mean, mmetsp, MMETSP_ID_paste, ncgr, NCGR_PEP_ID_paste, oceanography, office, paste, pep, phylum, phylum_max, preliminary, species, species_max, strain, strain_max, taxon, TAXON_ID_mean
attribute	NC_GLOBAL	license	String	https://www.bco-dmo.org/dataset/665427/license
attribute	NC_GLOBAL	metadata_source	String	https://www.bco-dmo.org/api/dataset/665427
attribute	NC_GLOBAL	Northernmost_Northing	double	77.8333
attribute	NC_GLOBAL	param_mapping	String	{'665427': {'lat': 'master - latitude', 'lon': 'master - longitude'}}
attribute	NC_GLOBAL	parameter_source	String	https://www.bco-dmo.org/mapserver/dataset/665427/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	subsetVariables	String	phylum_max
attribute	NC_GLOBAL	summary	String	Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP) location information on samples obtained on Gould (LMG1411) in the Western Antarctica Peninsula during 2014 (Polar Transcriptomes project)
attribute	NC_GLOBAL	title	String	[MMETSP locations and e-values] - Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP) location information on samples obtained on Gould (LMG1411) 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	phylum_max		String
attribute	phylum_max	bcodmo_name	String	phylum
attribute	phylum_max	description	String	Phylum
attribute	phylum_max	long_name	String	Phylum Max
attribute	phylum_max	units	String	unitless
variable	genus_max		String
attribute	genus_max	bcodmo_name	String	genus
attribute	genus_max	description	String	Genus
attribute	genus_max	long_name	String	Genus Max
attribute	genus_max	units	String	unitless
variable	species_max		String
attribute	species_max	bcodmo_name	String	species
attribute	species_max	description	String	Species
attribute	species_max	long_name	String	Species Max
attribute	species_max	units	String	unitless
variable	strain_max		String
attribute	strain_max	bcodmo_name	String	unknown
attribute	strain_max	description	String	Strain ID
attribute	strain_max	long_name	String	Strain Max
attribute	strain_max	units	String	unitless
variable	TAXON_ID_mean		int
attribute	TAXON_ID_mean	_FillValue	int	2147483647
attribute	TAXON_ID_mean	actual_range	int	3005, 1158023
attribute	TAXON_ID_mean	bcodmo_name	String	taxon
attribute	TAXON_ID_mean	description	String	Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP) taxon ID
attribute	TAXON_ID_mean	long_name	String	TAXON ID Mean
attribute	TAXON_ID_mean	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 mean; 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 mean; 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	lon_360		double
attribute	lon_360	_FillValue	double	NaN
attribute	lon_360	actual_range	double	2.1, 359.9975
attribute	lon_360	bcodmo_name	String	lon_360
attribute	lon_360	colorBarMaximum	double	180.0
attribute	lon_360	colorBarMinimum	double	-180.0
attribute	lon_360	description	String	360 Longitude; E is positive
attribute	lon_360	long_name	String	Longitude
attribute	lon_360	standard_name	String	longitude
attribute	lon_360	units	String	decimal degrees
variable	lat2		double
attribute	lat2	_FillValue	double	NaN
attribute	lat2	actual_range	double	-77.8333, 77.8333
attribute	lat2	bcodmo_name	String	latitude
attribute	lat2	colorBarMaximum	double	90.0
attribute	lat2	colorBarMinimum	double	-90.0
attribute	lat2	description	String	Latitude; N is positive
attribute	lat2	long_name	String	Latitude
attribute	lat2	nerc_identifier	String	https://vocab.nerc.ac.uk/collection/P09/current/LATX/
attribute	lat2	standard_name	String	latitude
attribute	lat2	units	String	decimal degrees
variable	evalue_paste		String
attribute	evalue_paste	bcodmo_name	String	unknown
attribute	evalue_paste	description	String	E-value
attribute	evalue_paste	long_name	String	Evalue Paste
attribute	evalue_paste	units	String	unitless
variable	evalue_mean		double
attribute	evalue_mean	_FillValue	double	NaN
attribute	evalue_mean	actual_range	double	0.0, 2.0E-8
attribute	evalue_mean	bcodmo_name	String	unknown
attribute	evalue_mean	description	String	Average E-value
attribute	evalue_mean	long_name	String	Evalue Mean
attribute	evalue_mean	units	String	unitless
variable	NCGR_PEP_ID_paste		String
attribute	NCGR_PEP_ID_paste	bcodmo_name	String	unknown
attribute	NCGR_PEP_ID_paste	description	String	National Center for Genome Resources (NCGR) protein ID
attribute	NCGR_PEP_ID_paste	long_name	String	NCGR PEP ID Paste
attribute	NCGR_PEP_ID_paste	units	String	unitless
variable	MMETSP_ID_paste		String
attribute	MMETSP_ID_paste	bcodmo_name	String	taxon
attribute	MMETSP_ID_paste	description	String	Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP) taxon ID
attribute	MMETSP_ID_paste	long_name	String	MMETSP ID Paste
attribute	MMETSP_ID_paste	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.