Accessing BCO-DMO data
log in    
Brought to you by BCO-DMO    

ERDDAP > info > bcodmo_dataset_745527

Title Sum-
Institution Dataset ID
   set  data   graph     files  public NCBI accession metadata for 18S rRNA gene tag sequences from DNA and RNA from samples
collected in coastal California in 2013 and 2014
   ?     I   M   background (external link) RSS Subscribe BCO-DMO bcodmo_dataset_745527

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 Samples were collected seasonally at the San Pedro Ocean Time-series (SPOT)
station at four depths (surface, subsurface chlorophyll maximum, 150 and 890
m).\u00a0The SPOT station was sampled from 5 m, the subsurface chlorophyll
maximum (SCM), 150 and 890 m using 10 L Niskin bottles mounted on a CTD
rosette, during regularly scheduled cruises

Seawater from all samples was sequentially pre-filtered through 200 \u03bcm
and 80 \u03bcm Nitex mesh to reduce abundances of multicellular eukaryotes
(metazoa). Near-surface and SCM seawater (2 L) and 150 and 890 m seawater (4
L) was filtered onto GF/F filters (nominal pore size 0.7 \u03bcm; Whatman,
International Ltd, Florham Park, NJ, USA) and immediately flash frozen in
liquid nitrogen for later DNA and RNA extraction.

Total DNA and RNA were extracted simultaneously from each sample using the All
Prep DNA/RNA Mini kit (Qiagen, Valencia, CA, USA, #80204). Genomic DNA was
removed during the RNA extraction with RNase-Free DNase reagents (Qiagen,
#79254). Total extracted RNA was checked for residual genomic DNA by
performing a polymerase chain reaction (PCR) using DNA specific primers to
ensure that no amplified products appeared when run on an agarose gel. RNA was
reverse transcribed into cDNA using iScript Reverse Transcription Supermix
with random hexamers (Bio-Rad Laboratories, Hercules, CA, USA, #170-8840).

The resulting cDNA and DNA from each sample were PCR amplified using V4
forward (5\u2032\u00a0-CCAGCA[GC]C[CT]GCGGTA ATTCC-3\u2032\u00a0) and reverse
(5\u2032\u00a0-ACTTTCGTTCTTGAT[CT][AG]A-3\u2032\u00a0) primers (Stoeck et al.
2010). Duplicate PCR reactions were performed in 50 \u03bcL volumes of: 1X
Phusion High-Fidelity DNA buffer, 1 unit of Phusion DNA polymerase (New
England Biolabs, Ipswich, MA, USA, #M0530S), 200 \u03bcM of dNTPs, 0.5 \u03bcM
of each V4 forward and reverse primer, 3% DMSO, 50 mM of MgCl and 5 ng of
either DNA or cDNA template per reaction. The PCR thermal cycler program
consisted of a 98\u25e6C denaturation step for 30 s, followed by 10 cycles of
10 s at 98\u25e6C, 30 s at 53\u25e6C and 30 s at 72\u25e6C, and then 15 cycles
of 10 s at 98\u25e6C, 30 s at 48\u25e6C and 30 s at 72\u25e6C, and a final
elongation step at 72\u25e6C for 10 min, as described in Rodr\u0131
\u0301guez-Mart\u0131 \u0301nez et al. (2012). PCR products were purified
(Qiagen, #28104) and duplicate samples were pooled. The \u223c400 bp cDNA and
DNA PCR products were quality checked on an Agilent Bioanalyzer 2100 (Agilent
Technologies, Santa Clara, CA).

Sampling Locations:
SPOT (33\u25e6 33\u2032 N, 118\u25e6 24\u2032 W) - surface, DCM, 150 m, and
890 m
Port of LA (33\u25e6 42.75\u2032 N, 118\u25e6 15.55\u2032 W) - surface
Catalina (33\u25e6 27.17\u2032 N, 118\u25e6 28.51\u2032 W)-surface

For protocols see:
attribute NC_GLOBAL awards_0_award_nid String 743048
attribute NC_GLOBAL awards_0_award_number String OCE-1737409
attribute NC_GLOBAL awards_0_data_url String http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1737409 (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 18S rRNA gene tag sequences
PI: David Caron
Data version 1: 2018-09-05
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 2018-09-04T20:29:24Z
attribute NC_GLOBAL date_modified String 2020-03-06T16:52:33Z
attribute NC_GLOBAL defaultDataQuery String &time<now
attribute NC_GLOBAL doi String 10.1575/1912/bco-dmo.745527.1
attribute NC_GLOBAL Easternmost_Easting double -118.26
attribute NC_GLOBAL geospatial_lat_max double 33.72
attribute NC_GLOBAL geospatial_lat_min double 33.45
attribute NC_GLOBAL geospatial_lat_units String degrees_north
attribute NC_GLOBAL geospatial_lon_max double -118.26
attribute NC_GLOBAL geospatial_lon_min double -118.48
attribute NC_GLOBAL geospatial_lon_units String degrees_east
attribute NC_GLOBAL infoUrl String https://www.bco-dmo.org/dataset/745527 (external link)
attribute NC_GLOBAL institution String BCO-DMO
attribute NC_GLOBAL instruments_0_acronym String Niskin bottle
attribute NC_GLOBAL instruments_0_dataset_instrument_nid String 745591
attribute NC_GLOBAL instruments_0_description String A Niskin bottle (a next generation water sampler based on the Nansen bottle) is a cylindrical, non-metallic water collection device with stoppers at both ends. The bottles can be attached individually on a hydrowire or deployed in 12, 24 or 36 bottle Rosette systems mounted on a frame and combined with a CTD. Niskin bottles are used to collect discrete water samples for a range of measurements including pigments, nutrients, plankton, etc.
attribute NC_GLOBAL instruments_0_instrument_external_identifier String https://vocab.nerc.ac.uk/collection/L22/current/TOOL0412/ (external link)
attribute NC_GLOBAL instruments_0_instrument_name String Niskin bottle
attribute NC_GLOBAL instruments_0_instrument_nid String 413
attribute NC_GLOBAL instruments_1_acronym String CTD SBE 911plus
attribute NC_GLOBAL instruments_1_dataset_instrument_nid String 745592
attribute NC_GLOBAL instruments_1_description String The Sea-Bird SBE 911plus is a type of CTD instrument package for continuous measurement of conductivity, temperature and pressure. The SBE 911plus includes the SBE 9plus Underwater Unit and the SBE 11plus Deck Unit (for real-time readout using conductive wire) for deployment from a vessel. The combination of the SBE 9plus and SBE 11plus is called a SBE 911plus. The SBE 9plus uses Sea-Bird's standard modular temperature and conductivity sensors (SBE 3plus and SBE 4). The SBE 9plus CTD can be configured with up to eight auxiliary sensors to measure other parameters including dissolved oxygen, pH, turbidity, fluorescence, light (PAR), light transmission, etc.). more information from Sea-Bird Electronics
attribute NC_GLOBAL instruments_1_instrument_external_identifier String https://vocab.nerc.ac.uk/collection/L22/current/TOOL0058/ (external link)
attribute NC_GLOBAL instruments_1_instrument_name String CTD Sea-Bird SBE 911plus
attribute NC_GLOBAL instruments_1_instrument_nid String 591
attribute NC_GLOBAL instruments_2_acronym String Automated Sequencer
attribute NC_GLOBAL instruments_2_dataset_instrument_nid String 745568
attribute NC_GLOBAL instruments_2_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_2_instrument_name String Automated DNA Sequencer
attribute NC_GLOBAL instruments_2_instrument_nid String 649
attribute NC_GLOBAL instruments_2_supplied_name String Illumina MiSeq
attribute NC_GLOBAL keywords String accession, bco, bco-dmo, biological, bioproject, bioproject_accession, chemical, data, dataset, depth, depth2, description, design, design_description, dmo, erddap, filename, filename2, filetpe2, filetype, instrument, instrument_model, latitude, layout, library, library_ID, library_layout, library_selection, library_source, library_strategy, link, longitude, management, model, name, oceanography, office, platform, preliminary, run, sample, sample_name, selection, source, sra, SRA_run_ID, SRA_run_link, SRA_study_ID, SRA_title, strategy, study, title
attribute NC_GLOBAL license String https://www.bco-dmo.org/dataset/745527/license (external link)
attribute NC_GLOBAL metadata_source String https://www.bco-dmo.org/api/dataset/745527 (external link)
attribute NC_GLOBAL Northernmost_Northing double 33.72
attribute NC_GLOBAL param_mapping String {'745527': {'lat': 'master - latitude', 'lon': 'master - longitude'}}
attribute NC_GLOBAL parameter_source String https://www.bco-dmo.org/mapserver/dataset/745527/parameters (external link)
attribute NC_GLOBAL people_0_affiliation String University of Southern California
attribute NC_GLOBAL people_0_affiliation_acronym String USC
attribute NC_GLOBAL people_0_person_name String David Caron
attribute NC_GLOBAL people_0_person_nid String 50524
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 Southern California
attribute NC_GLOBAL people_1_affiliation_acronym String USC
attribute NC_GLOBAL people_1_person_name String Sarah K Hu
attribute NC_GLOBAL people_1_person_nid String 745520
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 University of Southern California
attribute NC_GLOBAL people_2_affiliation_acronym String USC
attribute NC_GLOBAL people_2_person_name String Sarah K Hu
attribute NC_GLOBAL people_2_person_nid String 745520
attribute NC_GLOBAL people_2_role String Contact
attribute NC_GLOBAL people_2_role_type String related
attribute NC_GLOBAL people_3_affiliation String Woods Hole Oceanographic Institution
attribute NC_GLOBAL people_3_affiliation_acronym String WHOI BCO-DMO
attribute NC_GLOBAL people_3_person_name String Amber York
attribute NC_GLOBAL people_3_person_nid String 643627
attribute NC_GLOBAL people_3_role String BCO-DMO Data Manager
attribute NC_GLOBAL people_3_role_type String related
attribute NC_GLOBAL project String SPOT
attribute NC_GLOBAL projects_0_acronym String SPOT
attribute NC_GLOBAL projects_0_description String Planktonic marine microbial communities consist of a diverse collection of bacteria, archaea, viruses, protists (phytoplankton and protozoa) and small animals (metazoan). Collectively, these species are responsible for virtually all marine pelagic primary production where they form the basis of food webs and carry out a large fraction of respiratory processes. Microbial interactions include the traditional role of predation, but recent research recognizes the importance of parasitism, symbiosis and viral infection. Characterizing the response of pelagic microbial communities and processes to environmental influences is fundamental to understanding and modeling carbon flow and energy utilization in the ocean, but very few studies have attempted to study all of these assemblages in the same study. This project is comprised of long-term (monthly) and short-term (daily) sampling at the San Pedro Ocean Time-series (SPOT) site. Analysis of the resulting datasets investigates co-occurrence patterns of microbial taxa (e.g. protist-virus and protist-prokaryote interactions, both positive and negative) indicating which species consistently co-occur and potentially interact, followed by examination gene expression to help define the underlying mechanisms. This study augments 20 years of baseline studies of microbial abundance, diversity, rates at the site, and will enable detection of low-frequency changes in composition and potential ecological interactions among microbes, and their responses to changing environmental forcing factors. These responses have important consequences for higher trophic levels and ocean-atmosphere feedbacks. The broader impacts of this project include training graduate and undergraduate students, providing local high school student with summer lab experiences, and PI presentations at local K-12 schools, museums, aquaria and informal learning centers in the region. Additionally, the PIs advise at the local, county and state level regarding coastal marine water quality.
This research project is unique in that it is a holistic study (including all microbes from viruses to small metazoa) of microbial species diversity and ecological activities, carried out at the SPOT site off the coast of southern California. In studying all microbes simultaneously, this work aims to identify important ecological interactions among microbial species, and identify the basis(es) for those interactions. This research involves (1) extensive analyses of prokaryote (archaean and bacterial) and eukaryote (protistan and micro-metazoan) diversity via the sequencing of marker genes, (2) studies of whole-community gene expression by eukaryotes and prokaryotes in order to identify key functional characteristics of microorganismal groups and the detection of active viral infections, and (3) metagenomic analysis of viruses and bacteria to aid interpretation of transcriptomic analyses using genome-encoded information. The project includes exploratory metatranscriptomic analysis of poorly-understood aphotic and hypoxic-zone protists, to examine their stratification, functions and hypothesized prokaryotic symbioses.
attribute NC_GLOBAL projects_0_end_date String 2021-07
attribute NC_GLOBAL projects_0_geolocation String San Pedro Channel off the coast of Los Angeles
attribute NC_GLOBAL projects_0_name String Protistan, prokaryotic, and viral processes at the San Pedro Ocean Time-series
attribute NC_GLOBAL projects_0_project_nid String 743049
attribute NC_GLOBAL projects_0_start_date String 2017-08
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 33.45
attribute NC_GLOBAL standard_name_vocabulary String CF Standard Name Table v55
attribute NC_GLOBAL subsetVariables String bioproject_accession,SRA_study_ID,SRA_title,library_strategy,library_selection,library_layout,platform,instrument_model,filetype,filetpe2
attribute NC_GLOBAL summary String Raw DNA and RNA V4 tag sequences include spatially and temporally distinct samples from coastal California. Samples were collected in Niskin bottles with a CTD rosette at the San Pedro Ocean Time-series (SPOT) between April of 2013 and January of 2014. This dataset contains sequence data accession numbers and metadata for the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) database (SRA Study ID: SRP070577, BioProject: PRJNA311248).
attribute NC_GLOBAL title String NCBI accession metadata for 18S rRNA gene tag sequences from DNA and RNA from samples collected in coastal California in 2013 and 2014
attribute NC_GLOBAL version String 1
attribute NC_GLOBAL Westernmost_Easting double -118.48
attribute NC_GLOBAL xml_source String osprey2erddap.update_xml() v1.3
variable bioproject_accession   String  
attribute bioproject_accession bcodmo_name String unknown
attribute bioproject_accession description String NCBI BioProject identifier
attribute bioproject_accession long_name String Bioproject Accession
attribute bioproject_accession units String unitless
variable sample_name   String  
attribute sample_name bcodmo_name String unknown
attribute sample_name description String Sample name
attribute sample_name long_name String Sample Name
attribute sample_name units String unitless
variable SRA_run_ID   String  
attribute SRA_run_ID bcodmo_name String unknown
attribute SRA_run_ID description String SRA Run identifier
attribute SRA_run_ID long_name String SRA Run ID
attribute SRA_run_ID units String unitless
variable SRA_run_link   String  
attribute SRA_run_link bcodmo_name String unknown
attribute SRA_run_link description String URL for SRA Run Page at NCBI
attribute SRA_run_link long_name String SRA Run Link
attribute SRA_run_link units String unitless
variable library_ID   String  
attribute library_ID bcodmo_name String unknown
attribute library_ID description String SRA title
attribute library_ID long_name String Library ID
attribute library_ID units String unitless
variable SRA_study_ID   String  
attribute SRA_study_ID bcodmo_name String unknown
attribute SRA_study_ID description String SRA study identifier
attribute SRA_study_ID long_name String SRA Study ID
attribute SRA_study_ID units String unitless
variable SRA_title   String  
attribute SRA_title bcodmo_name String unknown
attribute SRA_title description String Descriptive title of SRA accession
attribute SRA_title long_name String SRA Title
attribute SRA_title units String unitless
variable library_strategy   String  
attribute library_strategy bcodmo_name String unknown
attribute library_strategy description String Library strategy ("AMPLICON")
attribute library_strategy long_name String Library Strategy
attribute library_strategy units String unitless
variable library_source   String  
attribute library_source bcodmo_name String unknown
attribute library_source description String Library source ("TRANSCRIPTOMIC" or "GENOMIC")
attribute library_source long_name String Library Source
attribute library_source units String unitless
variable library_selection   String  
attribute library_selection bcodmo_name String unknown
attribute library_selection description String Library selection ("PCR")
attribute library_selection long_name String Library Selection
attribute library_selection units String unitless
variable library_layout   String  
attribute library_layout bcodmo_name String unknown
attribute library_layout description String Library layout ("paired")
attribute library_layout long_name String Library Layout
attribute library_layout units String unitless
variable platform   String  
attribute platform bcodmo_name String platform
attribute platform description String Sequencing platform ("Illumina")
attribute platform long_name String Platform
attribute platform units String unitless
variable instrument_model   String  
attribute instrument_model bcodmo_name String unknown
attribute instrument_model description String Sequencing instrument model ("Illumina MiSeq")
attribute instrument_model long_name String Instrument Model
attribute instrument_model units String unitless
variable design_description   String  
attribute design_description bcodmo_name String unknown
attribute design_description description String Sequencing design description
attribute design_description long_name String Design Description
attribute design_description units String unitless
variable filetype   String  
attribute filetype bcodmo_name String unknown
attribute filetype description String Type of file 1
attribute filetype long_name String Filetype
attribute filetype units String unitless
variable filename   String  
attribute filename bcodmo_name String unknown
attribute filename description String Name of file 1
attribute filename long_name String Filename
attribute filename units String unitless
variable filetpe2   String  
attribute filetpe2 bcodmo_name String unknown
attribute filetpe2 description String Type of file 2
attribute filetpe2 long_name String Filetpe2
attribute filetpe2 units String unitless
variable filename2   String  
attribute filename2 bcodmo_name String unknown
attribute filename2 description String Name of file 2
attribute filename2 long_name String Filename2
attribute filename2 units String unitless
variable depth2   String  
attribute depth2 bcodmo_name String unknown
attribute depth2 description String Nominal depth ("Surface" or number of meters) of sample collection
attribute depth2 long_name String Depth
attribute depth2 standard_name String depth
attribute depth2 units String various
variable latitude   double  
attribute latitude _CoordinateAxisType String Lat
attribute latitude _FillValue double NaN
attribute latitude actual_range double 33.45, 33.72
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 of sample collection
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 -118.48, -118.26
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 of sample collection
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

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.

ERDDAP, Version 2.02
Disclaimers | Privacy Policy | Contact