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
attribute NC_GLOBAL acquisition_description String Seawater was collected from the San Pedro Ocean Time-series (SPOT) station off\nthe coast of Southern California near the surface (5 m), 150 and 890 m, in\nlate May 2015. Briefly, seawater was pre-filtered (80 mm) into 20 L carboys to\nminimize the presence of multicellular eukaryotes. Replicate samples (ranging\nin volume from 1.5-3.5 L) from each depth were filtered onto sterile GF/F\nfilters (nominal pore size 0.7 mm, Whatman, International Ltd. Florham Park,\nNJ). While we cannot avoid some impact that sample handling (i.e., bringing\nsamples to the surface) may have had on our results, filters were immediately\nplaced in 1.5 mL of lysis buffer and flash frozen in liquid nitrogen in < 40\nmin and away from light to minimize RNA degradation.\n \nTotal RNA was extracted from each filter using a DNA/RNA AllPrep kit (Qiagen,\nValencia, CA, #80204) with an in-line genomic DNA removal step (RNase-free\nDNase reagents, Qiagen #79254) (dx.doi.org/10.17504/protocols.io.hk3b4yn).\nExtracted RNA was quality checked and low biomass samples were pooled. Six\nreplicates were processed and sequenced from the surface, while pairs of\nfilters were pooled for either 150 or 890 m, yielding 3 and 4 replicates\nrespectively (Supporting Information Table S1). RNA concentrations were\nnormalized before library preparation (Supporting Information). ERCC spike-in\nwas added before sequence library preparation with Kapa\\u2019s Stranded mRNA\nlibrary preparation kit using poly-A tail selection beads to select for\neukaryotic mRNA (Kapa Biosystems, Inc., Wilmington, MA, #KK8420).\n \nAlso see:\n \n[https://www.protocols.io/view/sample-collection-from-the-field-for-\ndowns...](\\\\\"https://www.protocols.io/view/sample-collection-from-the-field-\nfor-downstream-mo-hisb4eehttps://www.protocols.io/view/rna-and-optional-dna-\nextraction-from-environmental-hk3b4yn\\\\\")\n \nThe associated assembly files can be found at Zenodo (see Hu, S. K. (2017),\nDOI:\\u00a010.5281/zenodo.1202041).\\u00a0 The assembly files were also\npublished in the journal publication Hu, et al. (2018).\n \nRelated code can be found in the github repository\n[https://github.com/shu251/SPOT_metatranscriptome.\\u00a0](\\\\\"https://github.com/shu251/SPOT_metatranscriptome.\\\\u00a0\\\\\")\nThe version of the code used for these publications can be found in the\nSupplemental Files section of this page.
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 Microbial eukaryotic focused metatranscriptome data \n    PI: David Caron \n    Data version 2: 2020-02-26
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 dataset_current_state String Final and no updates
attribute NC_GLOBAL date_created String 2018-09-04T20:19:13Z
attribute NC_GLOBAL date_modified String 2020-05-11T22:00:05Z
attribute NC_GLOBAL defaultDataQuery String &amp;time&lt;now
attribute NC_GLOBAL doi String 10.26008/1912/bco-dmo.745518.2
attribute NC_GLOBAL infoUrl String https://www.bco-dmo.org/dataset/745518 (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 773599
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 Automated Sequencer
attribute NC_GLOBAL instruments_1_dataset_instrument_description String HiSeq High Output 125 bp PE sequencing was performed at UPC Genome Core at University of Southern California, Los Angeles, CA (BioProject: PRJNA391503).
attribute NC_GLOBAL instruments_1_dataset_instrument_nid String 745534
attribute NC_GLOBAL instruments_1_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_1_instrument_name String Automated DNA Sequencer
attribute NC_GLOBAL instruments_1_instrument_nid String 649
attribute NC_GLOBAL instruments_1_supplied_name String HiSeq
attribute NC_GLOBAL keywords String accession, bco, bco-dmo, biological, bioproject, bioproject_accession, biosample, biosample_accession, chemical, data, dataset, description, design, design_description, dmo, erddap, filename, filename2, filetype, instrument, instrument_model, layout, library, library_ID, library_layout, library_selection, library_source, library_strategy, link, management, model, name, oceanography, office, platform, preliminary, run, sample, sample_name, selection, source, sra, SRA_run, SRA_run_link, SRA_study, strategy, study, title
attribute NC_GLOBAL license String https://www.bco-dmo.org/dataset/745518/license (external link)
attribute NC_GLOBAL metadata_source String https://www.bco-dmo.org/api/dataset/745518 (external link)
attribute NC_GLOBAL param_mapping String {'745518': {}}
attribute NC_GLOBAL parameter_source String https://www.bco-dmo.org/mapserver/dataset/745518/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 D. 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.\nThis 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 standard_name_vocabulary String CF Standard Name Table v55
attribute NC_GLOBAL subsetVariables String library_strategy,library_source,library_selection,library_layout,platform,instrument_model,design_description,filetype
attribute NC_GLOBAL summary String Seawater was collected via Niskin bottles mounted with a CTD from the San Pedro Ocean Time-series (SPOT) station off the coast of Southern California near the surface (5 m), 150 and 890 m, in late May 2015. Raw sequence data was generated as part of a metatranscriptome study targeting the protistan community.  Raw sequences are available at the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) database (SRA Study ID: SRP110974, BioProject: PRJNA391503).  Sequences for BioProject PRJNA608423 will be available at NCBI on Jan 1st, 2021.\\r\\n\\r\\nThese data were published in Hu et al. (2018).
attribute NC_GLOBAL title String [Microbial eukaryotic focused metatranscriptome data] - Microbial eukaryotic focused metatranscriptome data from seawater collected in coastal California in May of 2015 (Protistan, prokaryotic, and viral processes at the San Pedro Ocean Time-series)
attribute NC_GLOBAL version String 2
attribute NC_GLOBAL xml_source String osprey2erddap.update_xml() v1.5
variable SRA_run String
attribute SRA_run bcodmo_name String accession number
attribute SRA_run description String SRA Run identifier at NCBI
attribute SRA_run long_name String SRA Run
attribute SRA_run units String unitless
variable SRA_run_link String
attribute SRA_run_link bcodmo_name String external_link
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 SRA_study String
attribute SRA_study bcodmo_name String accession number
attribute SRA_study description String SRA study identifier at NCBI
attribute SRA_study long_name String SRA Study
attribute SRA_study units String unitless
variable bioproject_accession String
attribute bioproject_accession bcodmo_name String accession number
attribute bioproject_accession description String BioProject accesion number at NCBI
attribute bioproject_accession long_name String Bioproject Accession
attribute bioproject_accession units String unitless
variable biosample_accession String
attribute biosample_accession bcodmo_name String accession number
attribute biosample_accession description String BioSample accession number at NCBI
attribute biosample_accession long_name String Biosample Accession
attribute biosample_accession units String unitless
variable library_ID String
attribute library_ID bcodmo_name String sample_descrip
attribute library_ID description String SRA title
attribute library_ID long_name String Library ID
attribute library_ID units String unitless
variable title String
attribute title bcodmo_name String sample_descrip
attribute title description String Descriptive title of SRA accession
attribute title long_name String Title
attribute title units String unitless
variable sample_name String
attribute sample_name bcodmo_name String sample_descrip
attribute sample_name description String Sample name
attribute sample_name long_name String Sample Name
attribute sample_name units String unitless
variable library_strategy String
attribute library_strategy bcodmo_name String sample_descrip
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 sample_descrip
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 sample_descrip
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 sample_descrip
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 sample_descrip
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 sample_descrip
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 sample_descrip
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 sample_descrip
attribute filetype description String Type of files
attribute filetype long_name String Filetype
attribute filetype units String unitless
variable filename String
attribute filename bcodmo_name String file_name
attribute filename description String Name of file 1 (see NCBI for access)
attribute filename long_name String Filename
attribute filename units String unitless
variable filename2 String
attribute filename2 bcodmo_name String file_name
attribute filename2 description String Name of file 2 (see NCBI for access)
attribute filename2 long_name String Filename2
attribute filename2 units String unitless

 
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