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 Water was collected using Niskin bottles mounted on a CTD rosette. Biomass for\nmetatranscriptomic analysis was collected by filtration (after a 200 micron\npre-filtration) onto 47 mm, 1.2-micron pore size polycarbonate filters at <5\npsi for no longer than 15 min to minimize degradation. Filters were flash\nfrozen in liquid nitrogen and stored at -80 degrees C. Upon analysis, filters\nwere thawed and RNA was extracted using TRIzol reagent according to the\nmanufacturer\\u2019s protocol (Life Technologies). Metatranscriptome libraries\nwere constructed using 500 ng of total RNA and a TruSeq RNA Sample Preparation\nKit (Illumina; San Diego, CA) following the Low-Throughput protocol. The mean\nsize of the final libraries was confirmed to be between 359-420 base pairs\n(bp) using an Agilent Bioanalyzer 2100 (Santa Clara, CA). Libraries were\npaired-end sequenced (2x150 bp) on the Illumina HiSeq platform. ORFs were\nannotated via BLASTP alignment (e-value > 10-3) to a comprehensive protein\ndatabase, phyloDB, as well as screened for function de-novo by assigning\nPfams, TIGRfams and transmembrane tmHMMs with hmmer 3.0\n([http://hmmer.org/](\\\\\"http://hmmer.org/\\\\\")). PhyloDB 1.076 consists of\n24,509,327 peptides from 19,962 viral, 230 archaeal, 4,910 bacterial, and 894\neukaryotic taxa. It includes peptides at KEGG, GenBank, JGI, ENSEMBL, CAMERA,\nand various other repositories, as well as from the 410 taxa of the Marine\nMicrobial Eukaryotic Transcriptome Sequencing Project. Taxonomic annotation of\nORFs was also conducted via BLASTP to phyloDB.\n \nAll cruise related data are available publicly at the Biological and Chemical\nOceanography Data Management Office under project number 550825 ([https://www\n.bco-dmo.org/project/550825](\\\\\"https://www.bco-dmo.org/project/550825\\\\\")).\nThe metatranscriptomic data have been deposited in the NCBI sequence read\narchive (BioProject accession no. PRJNA528986: BioSample accession nos.\nSAMN11263616 - SAMN11263639 and SAMN11258802-SAMN11258825). Assembled contigs\nused in this study can also be found at\n[https://scripps.ucsd.edu/labs/aallen/data/](\\\\\"https://scripps.ucsd.edu/labs/aallen/data/\\\\\").\n \nUnassembled reads and rRNA data from this\nstudy:\\u00a0[https://www.ncbi.nlm.nih.gov/bioproject/PRJNA528986](\\\\\"https://www.ncbi.nlm.nih.gov/bioproject/PRJNA528986\\\\\")  \n Assembled contigs: See Supplemental Files.
attribute NC_GLOBAL awards_0_award_nid String 558197
attribute NC_GLOBAL awards_0_award_number String OCE-1333929
attribute NC_GLOBAL awards_0_data_url String http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1333929 (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 David L. Garrison
attribute NC_GLOBAL awards_0_program_manager_nid String 50534
attribute NC_GLOBAL cdm_data_type String Other
attribute NC_GLOBAL comment String DYEatom Metatranscriptome  \n   from RV/Point Sur cruise PS1312, DYEatom cruise, June-July 2013 \n   PI: K. Thamatrakoln (Rutgers) \n   version date: 2019-05-29
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 2019-05-23T19:52:52Z
attribute NC_GLOBAL date_modified String 2019-07-31T16:26:40Z
attribute NC_GLOBAL defaultDataQuery String &amp;time&lt;now
attribute NC_GLOBAL doi String 10.1575/1912/bco-dmo.768550.1
attribute NC_GLOBAL Easternmost_Easting double -121.981
attribute NC_GLOBAL geospatial_lat_max double 38.265
attribute NC_GLOBAL geospatial_lat_min double 36.455
attribute NC_GLOBAL geospatial_lat_units String degrees_north
attribute NC_GLOBAL geospatial_lon_max double -121.981
attribute NC_GLOBAL geospatial_lon_min double -123.969
attribute NC_GLOBAL geospatial_lon_units String degrees_east
attribute NC_GLOBAL geospatial_vertical_max double 55.5
attribute NC_GLOBAL geospatial_vertical_min double 1.6
attribute NC_GLOBAL geospatial_vertical_positive String down
attribute NC_GLOBAL geospatial_vertical_units String m
attribute NC_GLOBAL infoUrl String https://www.bco-dmo.org/dataset/768550 (external link)
attribute NC_GLOBAL institution String BCO-DMO
attribute NC_GLOBAL instruments_0_acronym String Automated Sequencer
attribute NC_GLOBAL instruments_0_dataset_instrument_nid String 768559
attribute NC_GLOBAL instruments_0_description String General term for a laboratory instrument used for deciphering the order of bases in a strand of DNA. Sanger sequencers detect fluorescence from different dyes that are used to identify the A, C, G, and T extension reactions. Contemporary or Pyrosequencer methods are based on detecting the activity of DNA polymerase (a DNA synthesizing enzyme) with another chemoluminescent enzyme. Essentially, the method allows sequencing of a single strand of DNA by synthesizing the complementary strand along it, one base pair at a time, and detecting which base was actually added at each step.
attribute NC_GLOBAL instruments_0_instrument_name String Automated DNA Sequencer
attribute NC_GLOBAL instruments_0_instrument_nid String 649
attribute NC_GLOBAL instruments_0_supplied_name String Illumina HiSeq platform
attribute NC_GLOBAL keywords String accession, bco, bco-dmo, bio, biological, BioProject_id, BioProject_type, BioSample, cast, chemical, collection, conductivity, cruise, cruise_id, ctd, CTD_cast, data, dataset, date, depth, depth_m, dmo, erddap, latitude, longitude, management, name, oceanography, office, package, Package_type, preliminary, project, sample, Sample_name, sonde, sra, SRA_id, station, temperature, time, type, version
attribute NC_GLOBAL license String https://www.bco-dmo.org/dataset/768550/license (external link)
attribute NC_GLOBAL metadata_source String https://www.bco-dmo.org/api/dataset/768550 (external link)
attribute NC_GLOBAL Northernmost_Northing double 38.265
attribute NC_GLOBAL param_mapping String {'768550': {'Lat': 'flag - latitude', 'depth_m': 'flag - depth', 'Long': 'flag - longitude'}}
attribute NC_GLOBAL parameter_source String https://www.bco-dmo.org/mapserver/dataset/768550/parameters (external link)
attribute NC_GLOBAL people_0_affiliation String Rutgers University
attribute NC_GLOBAL people_0_affiliation_acronym String Rutgers IMCS
attribute NC_GLOBAL people_0_person_name String Kimberlee Thamatrakoln
attribute NC_GLOBAL people_0_person_nid String 558200
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 J. Craig Venter Institute
attribute NC_GLOBAL people_1_affiliation_acronym String JCVI
attribute NC_GLOBAL people_1_person_name String Andrew E Allen
attribute NC_GLOBAL people_1_person_nid String 51525
attribute NC_GLOBAL people_1_role String Co-Principal Investigator
attribute NC_GLOBAL people_1_role_type String originator
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 Nancy Copley
attribute NC_GLOBAL people_2_person_nid String 50396
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 Diatom Silicification
attribute NC_GLOBAL projects_0_acronym String Diatom Silicification
attribute NC_GLOBAL projects_0_description String Description from NSF award abstract:\nDiatoms, unicellular, eukaryotic photoautotrophs, are among the most ecologically successful and functionally diverse organisms in the ocean. In addition to contributing one-fifth of total global primary productivity, diatoms are also the largest group of silicifying organisms in the ocean. Thus, diatoms form a critical link between the carbon and silicon (Si) cycles. The goal of this project is to understand the molecular regulation of silicification processes in natural diatom populations to better understand the processes controlling diatom productivity in the sea. Through culture studies and two research cruises, this research will couple classical measurements of silicon uptake and silica production with molecular and biochemical analyses of Silicification-Related Gene (SiRG) and protein expression. The proposed cruise track off the West Coast of the US will target gradients in Si and iron (Fe) concentrations with the following goals: 1) Characterize the expression pattern of SiRGs, 2) Correlate SiRG expression patterns to Si concentrations, silicon uptake kinetics, and silica production rates, 3) Develop a method to normalize uptake kinetics and silica production to SiRG expression levels as a more accurate measure of diatom activity and growth, 4) Characterize the diel periodicity of silica production and SiRG expression.\nIt is estimated that diatoms process 240 Teramoles of biogenic silica each year and that each molecule of silicon is cycled through a diatom 39 times before being exported to the deep ocean. Decades of oceanographic and field research have provided detailed insight into the dynamics of silicon uptake and silica production in natural populations, but a molecular understanding of the factors that influence silicification processes is required for further understanding the regulation of silicon and carbon fluxes in the ocean. Characterizing the genetic potential for silicification will provide new information on the factors that regulate the distribution of diatoms and influence in situ rates of silicon uptake and silica production. This research is expected to provide significant information about the molecular regulation of silicification in natural populations and the physiological basis of Si limitation in the sea.
attribute NC_GLOBAL projects_0_end_date String 2016-08
attribute NC_GLOBAL projects_0_geolocation String Oregon/California Coastal Upwelling Zone, between 34-44N and 120-124W
attribute NC_GLOBAL projects_0_name String Linking physiological and molecular aspects of diatom silicification in field populations
attribute NC_GLOBAL projects_0_project_nid String 558198
attribute NC_GLOBAL projects_0_start_date String 2013-09
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 36.455
attribute NC_GLOBAL standard_name_vocabulary String CF Standard Name Table v55
attribute NC_GLOBAL subsetVariables String BioProject_type,BioProject_id,Package_type,version,cruise_id
attribute NC_GLOBAL summary String Metadata for assembled contigs and ORFS from metatranscriptome analysis from CTD casts in the Monterey Bay area on RV/Point Sur cruise PS1312, June-July 2013. Assembled contigs files are also available; see Supplemental Files.
attribute NC_GLOBAL title String [DYEatom: Metatranscriptome accessions and assembled contigs] - DYEatom Metatranscriptome metadata from RV/Point Sur cruise PS1312 in the Monterey Bay area, June-July 2013 (Linking physiological and molecular aspects of diatom silicification in field populations)
attribute NC_GLOBAL version String 1
attribute NC_GLOBAL Westernmost_Easting double -123.969
attribute NC_GLOBAL xml_source String osprey2erddap.update_xml() v1.3
variable BioProject_type String
attribute BioProject_type bcodmo_name String exp_type
attribute BioProject_type description String NCBI BioProject type
attribute BioProject_type long_name String Bio Project Type
attribute BioProject_type units String unitless
variable BioProject_id String
attribute BioProject_id bcodmo_name String exp_id
attribute BioProject_id description String NCBI BioProject identifier
attribute BioProject_id long_name String Bio Project Id
attribute BioProject_id units String unitless
variable BioSample String
attribute BioSample bcodmo_name String accession number
attribute BioSample description String NCBI BioSample identifier
attribute BioSample long_name String Bio Sample
attribute BioSample units String unitless
variable Sample_name String
attribute Sample_name bcodmo_name String sample
attribute Sample_name description String NCBI Sample identifier
attribute Sample_name long_name String Sample Name
attribute Sample_name nerc_identifier String https://vocab.nerc.ac.uk/collection/P02/current/ACYC/ (external link)
attribute Sample_name units String unitless
variable SRA_id String
attribute SRA_id bcodmo_name String sample
attribute SRA_id description String NCBI SRA identifier
attribute SRA_id long_name String SRA Id
attribute SRA_id nerc_identifier String https://vocab.nerc.ac.uk/collection/P02/current/ACYC/ (external link)
attribute SRA_id units String unitless
variable Package_type String
attribute Package_type bcodmo_name String sample_type
attribute Package_type description String NCBI Package type
attribute Package_type long_name String Package Type
attribute Package_type units String unitless
variable version byte
attribute version _FillValue byte 127
attribute version actual_range byte 1, 1
attribute version bcodmo_name String unknown
attribute version description String NCBI version
attribute version long_name String Version
attribute version units String unitless
variable Accession String
attribute Accession bcodmo_name String accession number
attribute Accession description String NCBI Accession
attribute Accession long_name String Accession
attribute Accession units String unitless
variable ID int
attribute ID _FillValue int 2147483647
attribute ID actual_range int 11258802, 11263639
attribute ID bcodmo_name String accession number
attribute ID description String NCBI ID
attribute ID long_name String ID
attribute ID units String unitless
variable cruise_id String
attribute cruise_id bcodmo_name String cruise_id
attribute cruise_id description String cruise identifier
attribute cruise_id long_name String Cruise Id
attribute cruise_id units String unitless
variable CTD_cast String
attribute CTD_cast bcodmo_name String cast
attribute CTD_cast description String CTD cast number
attribute CTD_cast long_name String CTD Cast
attribute CTD_cast units String unitless
variable latitude double
attribute latitude _CoordinateAxisType String Lat
attribute latitude _FillValue double NaN
attribute latitude actual_range double 36.455, 38.265
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; north 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 -123.969, -121.981
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; east 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 source_name String Long
attribute longitude standard_name String longitude
attribute longitude units String degrees_east
variable Date_collection String
attribute Date_collection bcodmo_name String date
attribute Date_collection description String date of collection; formatted as yyyy-mm-dd
attribute Date_collection long_name String Date Collection
attribute Date_collection nerc_identifier String https://vocab.nerc.ac.uk/collection/P01/current/ADATAA01/ (external link)
attribute Date_collection source_name String Date_collection
attribute Date_collection time_precision String 1970-01-01
attribute Date_collection units String unitless
variable station byte
attribute station _FillValue byte 127
attribute station actual_range byte 2, 11
attribute station bcodmo_name String station
attribute station description String station number
attribute station long_name String Station
attribute station units String unitless
variable depth double
attribute depth _CoordinateAxisType String Height
attribute depth _CoordinateZisPositive String down
attribute depth _FillValue double NaN
attribute depth actual_range double 1.6, 55.5
attribute depth axis String Z
attribute depth bcodmo_name String depth
attribute depth colorBarMaximum double 8000.0
attribute depth colorBarMinimum double -8000.0
attribute depth colorBarPalette String TopographyDepth
attribute depth description String depth of sample
attribute depth ioos_category String Location
attribute depth long_name String Depth
attribute depth nerc_identifier String https://vocab.nerc.ac.uk/collection/P09/current/DEPH/ (external link)
attribute depth positive String down
attribute depth standard_name String depth
attribute depth units String m

 
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