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Title Sum-
Institution Dataset ID
   set  data   graph     files  public CTD data from 39 stations from R/V Cape Hatteras cruise CH0112 in the Northwest Atlantic
Continental Shelf in 2012 (CiliateSequencing project)
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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,.odvTxt
attribute NC_GLOBAL acquisition_description String 23 stations were sampled along a transect from Narragansett, RI to the shelf
break. 16 stations were sampled on the way back.

Header information from CTD files:
Sea-Bird SBE 9 Data File:
Software Version Seasave V 7.20a
Temperature SN = 0967
Conductivity SN = 0626
Number of Bytes Per Scan = 41
Number of Voltage Words = 4
Number of Scans Averaged by the Deck Unit = 1
Append System Time to Every Scan
attribute NC_GLOBAL awards_0_award_nid String 54721
attribute NC_GLOBAL awards_0_award_number String OCE-1129734
attribute NC_GLOBAL awards_0_data_url String http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1129734 (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 awards_1_award_nid String 54820
attribute NC_GLOBAL awards_1_award_number String OCE-1130033
attribute NC_GLOBAL awards_1_data_url String http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1130033 (external link)
attribute NC_GLOBAL awards_1_funder_name String NSF Division of Ocean Sciences
attribute NC_GLOBAL awards_1_funding_acronym String NSF OCE
attribute NC_GLOBAL awards_1_funding_source_nid String 355
attribute NC_GLOBAL awards_1_program_manager String David L. Garrison
attribute NC_GLOBAL awards_1_program_manager_nid String 50534
attribute NC_GLOBAL cdm_data_type String Other
attribute NC_GLOBAL comment String CTD Data from CH0112 Cruise
R/V Hatteras - July 06-09, 2012
PI: George B. McManus (UConn)
Co-PI: Laura A. Katz (Smith College)
Version: 07 June 2013
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 2013-06-07T17:07:46Z
attribute NC_GLOBAL date_modified String 2019-11-06T17:07:26Z
attribute NC_GLOBAL defaultDataQuery String &time<now
attribute NC_GLOBAL doi String 10.1575/1912/bco-dmo.3959.1
attribute NC_GLOBAL Easternmost_Easting double -71.4587
attribute NC_GLOBAL geospatial_lat_max double 41.2477
attribute NC_GLOBAL geospatial_lat_min double 39.7763
attribute NC_GLOBAL geospatial_lat_units String degrees_north
attribute NC_GLOBAL geospatial_lon_max double -71.4587
attribute NC_GLOBAL geospatial_lon_min double -71.4673
attribute NC_GLOBAL geospatial_lon_units String degrees_east
attribute NC_GLOBAL geospatial_vertical_max double 852.931
attribute NC_GLOBAL geospatial_vertical_min double 1.534
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/3959 (external link)
attribute NC_GLOBAL institution String BCO-DMO
attribute NC_GLOBAL instruments_0_acronym String CTD SBE 9
attribute NC_GLOBAL instruments_0_dataset_instrument_nid String 6179
attribute NC_GLOBAL instruments_0_description String The Sea-Bird SBE 9 is a type of CTD instrument package. The SBE 9 is the Underwater Unit and is most often combined with the SBE 11 Deck Unit (for real-time readout using conductive wire) when deployed from a research vessel. The combination of the SBE 9 and SBE 11 is called a SBE 911. The SBE 9 uses Sea-Bird's standard modular temperature and conductivity sensors (SBE 3 and SBE 4). The SBE 9 CTD can be configured with auxiliary sensors to measure other parameters including dissolved oxygen, pH, turbidity, fluorometer, altimeter, etc.). Note that in most cases, it is more accurate to specify SBE 911 than SBE 9 since it is likely a SBE 11 deck unit was used. more information from Sea-Bird Electronics
attribute NC_GLOBAL instruments_0_instrument_external_identifier String https://vocab.nerc.ac.uk/collection/L05/current/130/ (external link)
attribute NC_GLOBAL instruments_0_instrument_name String CTD Sea-Bird 9
attribute NC_GLOBAL instruments_0_instrument_nid String 488
attribute NC_GLOBAL instruments_0_supplied_name String CTD Sea-Bird 9
attribute NC_GLOBAL keywords String bco, bco-dmo, biological, chemical, cond, data, dataset, date, day, day_start, depth, dmo, erddap, fluor, iso, latitude, longitude, management, month, month_start, O2, oceanography, office, oxygen, preliminary, press, scan, sta, start, temp2, temperature, time, time_start, year
attribute NC_GLOBAL license String https://www.bco-dmo.org/dataset/3959/license (external link)
attribute NC_GLOBAL metadata_source String https://www.bco-dmo.org/api/dataset/3959 (external link)
attribute NC_GLOBAL Northernmost_Northing double 41.2477
attribute NC_GLOBAL param_mapping String {'3959': {'depth': 'flag - depth', 'lon_start': 'flag - longitude', 'ISO_DateTime_UTC': 'master - time', 'lat_start': 'flag - latitude'}}
attribute NC_GLOBAL parameter_source String https://www.bco-dmo.org/mapserver/dataset/3959/parameters (external link)
attribute NC_GLOBAL people_0_affiliation String University of Connecticut
attribute NC_GLOBAL people_0_affiliation_acronym String UConn - Avery Point
attribute NC_GLOBAL people_0_person_name String George B. McManus
attribute NC_GLOBAL people_0_person_nid String 51375
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 Smith College
attribute NC_GLOBAL people_1_person_name String Laura A. Katz
attribute NC_GLOBAL people_1_person_nid String 51376
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 Shannon Rauch
attribute NC_GLOBAL people_2_person_nid String 51498
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 CiliateSequencing
attribute NC_GLOBAL projects_0_acronym String CiliateSequencing
attribute NC_GLOBAL projects_0_description String The Ocean's biomass and diversity are predominantly microbial, yet this aspect of diversity remains underexplored. Efforts in recent years have begun to document microbial diversity in marine systems, and to elucidate the processes that structure assemblages across space and time. This project focuses on two important sister clades of microbial eukaryotes, the oligotrich and choreotrich ciliates. These organisms comprise a major component of planktonic food webs as they graze on phytoplankton, and are in turn eaten by zooplankton and larval fish.
Earlier molecular work on ciliate diversity relied on light microscopy, construction of clone libraries and Sanger sequencing. This revealed a high degree of cryptic diversity (similar species that are genetically distinct), which is surprising, given the long-held idea that all microbes are globally distributed and that few species exist, at least as compared to animals and plants. This past work also showed that ciliate assemblages contain a few highly abundant forms and many rare ones, consistent with the concept of a "rare biosphere". However, these methods are limited by high costs of both labor and materials, so that efforts to sample any local assemblage comprehensively usually resulted in undersaturation (repeated sampling continued to uncover new species). Next generation approaches are needed to truly assess the depths of biodiversity in planktonic ciliates.
This project brings together investigators with strengths in ecology, taxonomy and oceanography (PI McManus) and in molecular evolution, systematics and bioinformatics (PI Katz). Pyrosequencing will be used to sample the oligotrich and choreotrich ciliates ’to exhaustion’ in coastal environments. Denaturing gradient gel electrophoresis (DGGE), a technique that generates a fingerprint of the diversity in a sample, will be used to pre-select samples for pyrosequencing based on where strong gradients are observed in the composition of assemblages in relation to environmental factors (density fronts, thermolclines, etc.). Using these approaches, combined with the informatics pipeline already in place, this project will address three specific objectives:
Objective 1. Determine the spatial scale of variability in ciliate diversity by measuring how ciliate assemblages change over meter, kilometer, 100 km, and basin scales.
Objective 2. Assess the contributions of different size classes of ciliates to overall assemblage diversity.
Objective 3. Experimentally evaluate factors that control the temporal shift of individual species from rarity to commonness in a natural assemblage, and vice versa.
Note: See the related collaborative project, "Patterns of diversity in planktonic ciliates: spatio-temporal scales and community assembly in the coastal ocean", funded by awards OCE-1435515 and OCE-1436003.
attribute NC_GLOBAL projects_0_end_date String 2015-08
attribute NC_GLOBAL projects_0_geolocation String NW Atlantic Continental Shelf
attribute NC_GLOBAL projects_0_name String Diversity and dynamics of planktonic ciliates - what can next-generation sequencing technologies tell us?
attribute NC_GLOBAL projects_0_project_nid String 2164
attribute NC_GLOBAL projects_0_project_website String http://microzooplankton.uconn.edu (external link)
attribute NC_GLOBAL projects_0_start_date String 2012-07
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 39.7763
attribute NC_GLOBAL standard_name_vocabulary String CF Standard Name Table v55
attribute NC_GLOBAL subsetVariables String month_start,year
attribute NC_GLOBAL summary String CTD data from 39 stations from R/V Cape Hatteras cruise CH0112 in the Northwest Atlantic Continental Shelf in 2012.
attribute NC_GLOBAL time_coverage_end String 2012-07-09T10:54:22Z
attribute NC_GLOBAL time_coverage_start String 2012-07-06T22:19:17Z
attribute NC_GLOBAL title String CTD data from 39 stations from R/V Cape Hatteras cruise CH0112 in the Northwest Atlantic Continental Shelf in 2012 (CiliateSequencing project)
attribute NC_GLOBAL version String 1
attribute NC_GLOBAL Westernmost_Easting double -71.4673
attribute NC_GLOBAL xml_source String osprey2erddap.update_xml() v1.3
variable sta   byte  
attribute sta _FillValue byte 127
attribute sta actual_range byte 1, 39
attribute sta bcodmo_name String sta
attribute sta description String Station ID number.
attribute sta long_name String Sta
attribute sta units String unitless
variable latitude   double  
attribute latitude _CoordinateAxisType String Lat
attribute latitude _FillValue double NaN
attribute latitude actual_range double 39.7763, 41.2477
attribute latitude axis String Y
attribute latitude bcodmo_name String lat_start
attribute latitude colorBarMaximum double 90.0
attribute latitude colorBarMinimum double -90.0
attribute latitude description String Latitude at start of CTD cast. North = 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 source_name String lat_start
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 -71.4673, -71.4587
attribute longitude axis String X
attribute longitude bcodmo_name String lon_start
attribute longitude colorBarMaximum double 180.0
attribute longitude colorBarMinimum double -180.0
attribute longitude description String Longitude at start of CTD cast. West = negative.
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 lon_start
attribute longitude standard_name String longitude
attribute longitude units String degrees_east
variable month_start   String  
attribute month_start bcodmo_name String month_start
attribute month_start description String 2-digit month at start of cast.
attribute month_start long_name String Month Start
attribute month_start units String mm (01 to 12)
variable day_start   String  
attribute day_start bcodmo_name String day_start
attribute day_start description String 2-digit day of month at start of cast.
attribute day_start long_name String Day Start
attribute day_start units String dd (01 to 31)
variable year   short  
attribute year _FillValue short 32767
attribute year actual_range short 2012, 2012
attribute year bcodmo_name String year
attribute year description String 4-digit year in YYYY format.
attribute year long_name String Year
attribute year nerc_identifier String https://vocab.nerc.ac.uk/collection/P01/current/YEARXXXX/ (external link)
attribute year units String unitless
variable time_start   String  
attribute time_start bcodmo_name String time_start
attribute time_start description String Time at start of cast (UTC).
attribute time_start long_name String Time Start
attribute time_start units String HHMM.mm
variable time   double  
attribute time _CoordinateAxisType String Time
attribute time actual_range double 1.341613157E9, 1.341831262E9
attribute time axis String T
attribute time bcodmo_name String ISO_DateTime_UTC
attribute time description String Date/time (UTC) at start of cast formatted to ISO 8601 standard.
attribute time ioos_category String Time
attribute time long_name String ISO Date Time UTC
attribute time nerc_identifier String https://vocab.nerc.ac.uk/collection/P01/current/DTUT8601/ (external link)
attribute time source_name String ISO_DateTime_UTC
attribute time standard_name String time
attribute time time_origin String 01-JAN-1970 00:00:00
attribute time time_precision String 1970-01-01T00:00:00Z
attribute time units String seconds since 1970-01-01T00:00:00Z
variable press   float  
attribute press _FillValue float NaN
attribute press actual_range float 1.546, 861.284
attribute press bcodmo_name String pressure
attribute press description String Pressure
attribute press long_name String Press
attribute press nerc_identifier String https://vocab.nerc.ac.uk/collection/P01/current/PRESPR01/ (external link)
attribute press units String decibars
variable depth   double  
attribute depth _CoordinateAxisType String Height
attribute depth _CoordinateZisPositive String down
attribute depth _FillValue double NaN
attribute depth actual_range double 1.534, 852.931
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
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
variable cond   float  
attribute cond _FillValue float NaN
attribute cond actual_range float 0.006806, 5.082737
attribute cond bcodmo_name String conductivity
attribute cond description String Conductivity in Siemens per meter.
attribute cond long_name String Cond
attribute cond nerc_identifier String https://vocab.nerc.ac.uk/collection/P02/current/CNDC/ (external link)
attribute cond units String S/m
variable temp   float  
attribute temp _FillValue float NaN
attribute temp actual_range float 4.7069, 24.8754
attribute temp bcodmo_name String temperature
attribute temp description String Temperature (degrees Celsius) from primary sensor.
attribute temp long_name String Temperature
attribute temp nerc_identifier String https://vocab.nerc.ac.uk/collection/P01/current/TEMPP901/ (external link)
attribute temp units String degrees C
variable temp2   float  
attribute temp2 _FillValue float NaN
attribute temp2 actual_range float 4.7051, 25.0675
attribute temp2 bcodmo_name String temp2
attribute temp2 description String Temperature (degrees Celsius) from secondary sensor.
attribute temp2 long_name String Temp2
attribute temp2 nerc_identifier String https://vocab.nerc.ac.uk/collection/P01/current/TEMPS601/ (external link)
attribute temp2 units String degrees C
variable fluor   float  
attribute fluor _FillValue float NaN
attribute fluor actual_range float 0.0059, 1.6435
attribute fluor bcodmo_name String fluorescence
attribute fluor description String Chlorophyll fluorescence (micrograms per liter) measured by Chelsea Aqua 3 sensor. Fluorescence values should be interpreted as "arbitrary units" because calibrations have not been applied.
attribute fluor long_name String Fluor
attribute fluor nerc_identifier String https://vocab.nerc.ac.uk/collection/P01/current/CPHLPM01/ (external link)
attribute fluor units String ug/L
variable O2   float  
attribute O2 _FillValue float NaN
attribute O2 actual_range float 4.15016, 10.49208
attribute O2 bcodmo_name String Dissolved_Oxygen
attribute O2 description String Oxygen (milligrams per liter) measured by SBE 43 sensor.
attribute O2 long_name String O2
attribute O2 units String mg/L
variable scan   short  
attribute scan _FillValue short 32767
attribute scan actual_range short 1, 27611
attribute scan bcodmo_name String scan
attribute scan description String CTD scan number.
attribute scan long_name String Scan
attribute scan units String integer

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.

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