BCO-DMO ERDDAP
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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\nalong the PalmerLTER sampling grid in 2013 and 2014. Isolations were performed\nusing an Olympus CKX41 inverted microscope by single cell isolation with a\nmicropipette (Anderson 2005). Diatom species were identified by morphological\ncharacterization and 18S rRNA gene (rDNA) sequencing. DNA was extracted with\nthe DNeasy Plant Mini Kit according to the manufacturer\\u2019s protocols\n(Qiagen). Amplification of the nuclear 18S rDNA region was achieved with\nstandard PCR protocols using eukaryotic-specific, universal 18S forward and\nreverse primers. Primer sequences were obtained from Medlin et al. (1982). The\nlength of the region amplified is approximately 1800 base pairs (bp\n).\\u00a0Pseudo-nitzschia\\u00a0species are often difficult to identify by their\n18S rDNA sequence, therefore, additional support of the taxonomic\nidentification of\\u00a0P.\\u00a0subcurvata\\u00a0was provided through sequencing\nof the 18S-ITS1-5.8S regions. Amplification of this region was performed with\nthe 18SF-euk and 5.8SR_euk primers of Hubbard et al. (2008). PCR products were\npurified using either QIAquick PCR Purification Kit (Qiagen) or ExoSAP-IT\n(Affymetrix) and sequenced by Sanger DNA sequencing (Genewiz). Sequences were\nedited using Geneious Pro software\n([http://www.geneious.com](\\\\\"http://www.geneious.com\\\\\"), Kearse et al.,\n2012) and BLASTn sequence homology searches were performed against the NCBI\nnucleotide non-redundant (nr) database to determine species with a cutoff\nidentity of 98%.\n \nDiatom phylogenetic analysis was performed with Geneious Pro and included 71\nadditional diatom 18S rDNA sequences from publically available genomes and\ntranscriptomes, including those in the MMETSP database. Diatom sequences were\ntrimmed to the same length and aligned with MUSCLE (Edgar 2004). A\nphylogenetic tree was created in Mega with the Maximum-likelihood method of\ntree reconstruction, the Jukes-Cantor genetic distance model (Jukes and Cantor\n1969), and 100 bootstrap replicates.\n \nIsolates were maintained at 4 deg C in constant irradiance at intensities of\neither 10\\u00a0umol\\u00a0photons m-2\\u00a0s-1\\u00a0(low light) or\n90\\u00a0umol\\u00a0photons m-2\\u00a0s-1\\u00a0(growth saturating light) and with\nmedia containing high and low iron concentrations. Cultures were grown in the\nsynthetic seawater medium, AQUIL, enriched with filter sterilized vitamin and\ntrace metal ion buffer containing 100\\u00a0umol\\u00a0L-1\\u00a0EDTA. The growth\nmedia also contained 300 \\u03bcmol L-1\\u00a0nitrate,\n200\\u00a0umol\\u00a0L-1\\u00a0silicic acid and\n20\\u00a0umol\\u00a0L-1\\u00a0phosphate. Premixed Fe-EDTA (1:1) was added\nseparately for total iron concentrations of either 1370 nmol L-1\\u00a0or 3.1\nnmol L-1. Cultures were grown in acid-washed 28 mL polycarbonate centrifuge\ntubes (Nalgene) and maintained in exponential phase by dilution. Specific\ngrowth rates of successive transfers were calculated from the linear\nregression of the natural\\u00a0log of\\u00a0in\nvivo\\u00a0chlorophyll\\u00a0a\\u00a0fluorescence using a Turner 10-AU\nfluorometer (Brand et al. 1981).\\u00a0\\u200b\n \n\\u00a0
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 (external link)
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 Isolate Information \n  Adrian Marchetti, PI \n  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/ (external link)
attribute NC_GLOBAL data_source String extract_data_as_tsv version 2.3  19 Dec 2019
attribute NC_GLOBAL date_created String 2016-11-18T22:29:42Z
attribute NC_GLOBAL date_modified String 2019-04-18T13:56:27Z
attribute NC_GLOBAL defaultDataQuery String &time<now
attribute NC_GLOBAL doi String 10.1575/1912/bco-dmo.665288.1
attribute NC_GLOBAL Easternmost_Easting double -67.337
attribute NC_GLOBAL geospatial_lat_max double -66.254
attribute NC_GLOBAL geospatial_lat_min double -68.112
attribute NC_GLOBAL geospatial_lat_units String degrees_north
attribute NC_GLOBAL geospatial_lon_max double -67.337
attribute NC_GLOBAL geospatial_lon_min double -72.739
attribute NC_GLOBAL geospatial_lon_units String degrees_east
attribute NC_GLOBAL infoUrl String https://www.bco-dmo.org/dataset/665288 (external link)
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 665295
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).\n\nInverted 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.\n\nThe 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/ (external link)
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 665298
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 accession, accession_link, accession_number, bank, bco, bco-dmo, best, biological, chemical, data, dataset, diatoms, dmo, erddap, gen, GenBank_bestHit, hit, latitude, link, longitude, lter, management, number, oceanography, office, palmer, PalmerLTER_station, percent, percentSimilarity_bestHit, polar, polar_diatoms, preliminary, similarity, station, strain, strain_ID
attribute NC_GLOBAL license String https://www.bco-dmo.org/dataset/665288/license (external link)
attribute NC_GLOBAL metadata_source String https://www.bco-dmo.org/api/dataset/665288 (external link)
attribute NC_GLOBAL Northernmost_Northing double -66.254
attribute NC_GLOBAL param_mapping String {'665288': {'lat': 'master - latitude', 'lon': 'master - longitude'}}
attribute NC_GLOBAL parameter_source String https://www.bco-dmo.org/mapserver/dataset/665288/parameters (external link)
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.\nAlthough 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 (external link)
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 -68.112
attribute NC_GLOBAL standard_name_vocabulary String CF Standard Name Table v55
attribute NC_GLOBAL summary String Isolate information on genes found in samples collected on the Gould (LMG1411) cruise in the Western Antarctica Peninsula in 2014 (Polar Transcriptomes project).
attribute NC_GLOBAL title String Isolate information on genes found in samples collected on the Gould (LMG1411) cruise in the Western Antarctica Peninsula in 2014 (Polar Transcriptomes project).
attribute NC_GLOBAL version String 1
attribute NC_GLOBAL Westernmost_Easting double -72.739
attribute NC_GLOBAL xml_source String osprey2erddap.update_xml() v1.3
variable polar_diatoms String
attribute polar_diatoms bcodmo_name String species
attribute polar_diatoms description String Species names
attribute polar_diatoms long_name String Polar Diatoms
attribute polar_diatoms units String unitless
variable strain_ID String
attribute strain_ID bcodmo_name String sample
attribute strain_ID description String Strain ID number
attribute strain_ID long_name String Strain ID
attribute strain_ID nerc_identifier String https://vocab.nerc.ac.uk/collection/P02/current/ACYC/ (external link)
attribute strain_ID units String unitless
variable PalmerLTER_station String
attribute PalmerLTER_station bcodmo_name String sta
attribute PalmerLTER_station description String Palmer LTER station number
attribute PalmerLTER_station long_name String Palmer LTER Station
attribute PalmerLTER_station units String unitless
variable latitude double
attribute latitude _CoordinateAxisType String Lat
attribute latitude _FillValue double NaN
attribute latitude actual_range double -68.112, -66.254
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/ (external link)
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 -72.739, -67.337
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/ (external link)
attribute longitude standard_name String longitude
attribute longitude units String degrees_east
variable GenBank_bestHit String
attribute GenBank_bestHit bcodmo_name String accession number
attribute GenBank_bestHit description String Accession number of best hit in GenBank
attribute GenBank_bestHit long_name String Gen Bank Best Hit
attribute GenBank_bestHit units String unitless
variable percentSimilarity_bestHit byte
attribute percentSimilarity_bestHit _FillValue byte 127
attribute percentSimilarity_bestHit actual_range byte 98, 100
attribute percentSimilarity_bestHit bcodmo_name String unknown
attribute percentSimilarity_bestHit colorBarMaximum double 100.0
attribute percentSimilarity_bestHit colorBarMinimum double 0.0
attribute percentSimilarity_bestHit description String Percent similarity of sequence to the best hit
attribute percentSimilarity_bestHit long_name String Percent Similarity Best Hit
attribute percentSimilarity_bestHit units String percent
variable accession_number String
attribute accession_number bcodmo_name String accession number
attribute accession_number description String NBII Accession number
attribute accession_number long_name String Accession Number
attribute accession_number units String unitless
variable accession_link String
attribute accession_link bcodmo_name String accession number
attribute accession_link description String Accession link
attribute accession_link long_name String Accession Link
attribute accession_link units String unitless

 
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