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 \nIllumina TruSeq adapters and poly-A tails were trimmed from raw reads using\nthe Fastx_toolkit clipper function. Fastq_quality_filter was used to remove\npoor quality sequences, such that remaining sequences had a minimum quality\nscore of 20 with a minimum of 80% of bases within a\\u00a0read\\u00a0meeting\nthis quality score requirement. Any remaining raw sequences less than 50 base\npairs in length were also removed. Merged files were assembled\\u00a0de\nnovo\\u00a0using Trinity (Grabherr et al. 2011). The resulting assembly was\nfiltered to remove contigs less than 200 bp in length. Trinity-assembled\ncontigs which exhibited sequence overlap were grouped into isogroups which\nwere then used for sequence homology searches (BLASTx E-value \\u2264 10-4)\nagainst the Kyoto Encyclopedia of Genes and Genomes (KEGG) databases (Kanehisa\n2006).\n \nBUSCO (Benchmarking Universal Single-Copy Orthologs) was used to assess the\ncompleteness of genomes and transcriptomes based on sets of\\u00a0single\ncopy\\u00a0orthologous groups derived from OrthoDB that are highly conserved\nwithin multiple lineages (Felipe et al. 2015). Completed, duplicated and\nfragmented orthologs were determined by meeting an \\u2018expected score\\u2019\nand having aligned sequences within two standard deviations of the BUSCO\ngene\\u2019s length.\\u00a0A second\\u00a0metric of completeness was performed by\nevaluating conserved pathways, such as the ribosome and spliceosome, using the\nsingle-directional\\u00a0best-hit\\u00a0method in the KEGG Automatic Annotation\nServer (KAAS) (Moriya et al. 2007).\\u00a0Finally\\u00a0contiguity,\\u00a0was\ncalculated at the 0.75 level as according to Martin and Wang (2011) with\ncustom scripts.\n \nFor each transcriptome, unassembled sequence reads were aligned to the final\nTrinity assembly using Bowtie 2 (Langmead 2012). Mapped reads were normalized\nby the Reads per Kilobase per Million reads method (RPKM) (Mortazavi et al.\n2008).\n \nGene biogeographical distributions -\\u00a020 genes of interest were selected\nin the study to investigate the molecular basis of iron and light limitation\nin polar diatoms. Reference sequences for each of these genes were obtained\nfrom the\\u00a0F.\\u00a0cylindrus\\u00a0and\\u00a0P.\\u00a0tricornutum\\u00a0JGI\ngenome portals\nand\\u00a0T.\\u00a0pseudonana\\u00a0and\\u00a0T.\\u00a0oceanica\\u00a0NCBI and\nGenBank repositories. Reference sequences were identified in the\ntranscriptomes by translated nucleotide homology searches (tBLASTn) with an\ne-value cutoff of <10-5. A reciprocal tBLASTn homology search was performed\nfor each transcriptome against the KEGG GENES database, using the single-\ndirectional\\u00a0best-hit\\u00a0method in the KAAS online tool to ensure\nconsistent gene annotations (Moriya et al. 2007).\n \nSubsequently, reference sequences were identified in the MMETSP protein\ndatabase by BLASTp (e-value <10-5) homology searches among the diatom\ntranscriptomes. The transcriptomes and their associated latitude and longitude\nwere obtained from iMicrobe Data Commons (Project Code CAM_P_0001000) and the\nNational Center for Marine Algae and Microbiota (NCMA). Custom Matlab scripts\nallowed global biogeographical distribution of key genes of interest to be\nmapped.
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 MMETSP Location Data \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 2016-11-21T20:24:33Z
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 (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 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).\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 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 (external link)
attribute NC_GLOBAL metadata_source String https://www.bco-dmo.org/api/dataset/665427 (external link)
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 (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 -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/ (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 -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/ (external link)
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/ (external link)
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

 
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