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 Thaumarchaea transcriptomes sequences.
attribute NC_GLOBAL awards_0_award_nid String 555306
attribute NC_GLOBAL awards_0_award_number String OCE-1259994
attribute NC_GLOBAL awards_0_data_url String http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1259994 (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 555311
attribute NC_GLOBAL awards_1_award_number String OCE-1260006
attribute NC_GLOBAL awards_1_data_url String http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1260006 (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 Thaumarchaea transcriptomes \n  C. Dupont & A. Santoro, PIs \n  Version 10 July 2018
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 2018-07-10T18:08:40Z
attribute NC_GLOBAL date_modified String 2019-06-12T13:34:50Z
attribute NC_GLOBAL defaultDataQuery String &time<now
attribute NC_GLOBAL doi String 10.1575/1912/bco-dmo.739636.1
attribute NC_GLOBAL infoUrl String https://www.bco-dmo.org/dataset/739636 (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_description String Used to identify samples
attribute NC_GLOBAL instruments_0_dataset_instrument_nid String 739746
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 NextSEQ 500
attribute NC_GLOBAL keywords String accession, bco, bco-dmo, biological, chemical, data, dataset, dmo, erddap, management, name, oceanography, office, organism, preliminary, sample, Sample_Name, strain, tax, Tax_ID
attribute NC_GLOBAL license String https://www.bco-dmo.org/dataset/739636/license (external link)
attribute NC_GLOBAL metadata_source String https://www.bco-dmo.org/api/dataset/739636 (external link)
attribute NC_GLOBAL param_mapping String {'739636': {}}
attribute NC_GLOBAL parameter_source String https://www.bco-dmo.org/mapserver/dataset/739636/parameters (external link)
attribute NC_GLOBAL people_0_affiliation String J. Craig Venter Institute
attribute NC_GLOBAL people_0_affiliation_acronym String JCVI
attribute NC_GLOBAL people_0_person_name String Christopher Dupont
attribute NC_GLOBAL people_0_person_nid String 555309
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 California-Santa Barbara
attribute NC_GLOBAL people_1_affiliation_acronym String UCSB
attribute NC_GLOBAL people_1_person_name String Alyson Santoro
attribute NC_GLOBAL people_1_person_nid String 555313
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 J. Craig Venter Institute
attribute NC_GLOBAL people_2_affiliation_acronym String JCVI
attribute NC_GLOBAL people_2_person_name String Christopher Dupont
attribute NC_GLOBAL people_2_person_nid String 555309
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 Hannah Ake
attribute NC_GLOBAL people_3_person_nid String 650173
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 AmoA Archaea
attribute NC_GLOBAL projects_0_acronym String AmoA Archaea
attribute NC_GLOBAL projects_0_description String NSF award abstract:\nIntellectual Merit. How organisms respond to their physical and chemical and environment is a central question in marine ecology. For microbes living in the mesopelagic - the ocean's \"twilight zone\" - an efficient response is particularly important to capitalize on the intermittent delivery of organic and inorganic compounds sinking from the surface ocean. These organisms must have a suite of metabolic and regulatory strategies used to cope with environmental variability, but these strategies are largely unknown. Understanding when and why metabolic genes are expressed is critical to our understanding of nutrient remineralization in the ocean. Marine group 1 (MG1) archaea are ubiquitous, abundant microbes in the meso- and bathypelagic and promising model organisms for investigating these questions. MG1 archaea are chemolithoautotrophs that oxidize ammonia for energy and fix carbon for biomass, and as such, play a central role in the ocean's coupled carbon and nitrogen cycles. Though MG1 have historically eluded cultivation, recent efforts have been successful at bringing representative MG1 archaea from the open ocean into culture and demonstrating their importance in the production of the greenhouse gas nitrous oxide. This project takes advantage of unique MG1 cultures and the recently sequenced draft genome of one of the organisms - strain CN25 - to investigate the physiological and transcriptional responses of MG1 archaea to variations in their chemical environment, specifically:\n1. Comparative transcriptomics of CN25 cells grown under a range of energy availability and nitrosative stress will identify select genes that can be used to diagnose the physiological state of natural populations\n2. Improvements in the genomic and transcriptomic knowledge of MG1 archaea will facilitate a thorough reinterpretation of existing metagenomic and metatranscriptomic datasets, as well as provide a better contextual understanding in future studies\nThe investigators will conduct comparative transcriptomics of CN25 cells harvested in mid-exponential growth and stationary phase versus starved cells. Transcriptomes of cells grown at high nitrate concentrations and low pO2 with those grown in standard conditions will be characterized. A strand-specific, high-density RNAseq approach will be used to examine the expression of putative ORFs, polycistronic operons, and small RNAs, which, in addition to gene expression profiling, has the ancillary benefit of improving genome annotation. Finally, the investigators will sequence the genomes of two additional MG1 strains isolated from the open ocean, as well as single cells from environmental surveys, and leverage the combination with the CN25 genome to reanalyze available metagenomic and metatranscriptomic datasets. The results will define the transcriptional response of a model mesopelagic microbe to a range of chemical environments, and show how the physicochemical environment induces changes in gene expression and gene content that result in greenhouse gas production. This work will rapidly generate new knowledge of how some of the most ubiquitous, yet heretofore elusive, microorganisms respond to geochemical variability and shape our evolving understanding of the marine nitrogen cycle.\nBroader Impacts. The scientific and societal impact of the project will be to elucidate the mechanisms of greenhouse gas production in a model marine organism that is of broad interest to biological and chemical oceanographers. Transcriptome sequencing will improve the assembly of the CN25 genome, the first genome of an MG1 archaeon from the open ocean. Both the genome and transcriptomes will be important references for researchers using metagenomics, metatranscriptomics, and metaproteomics in the ocean, as these techniques are reliant on a knowledgebase composed of both DNA sequence and physiology. Thus, the results add value to both existing and future studies. The proposed research will advance education, teaching, and training for the next generation of marine scientists by providing support for two early-career investigators, one postdoctoral researcher, and a secondary school teacher.
attribute NC_GLOBAL projects_0_end_date String 2018-03
attribute NC_GLOBAL projects_0_geolocation String Epipelagic and mesopelagic, Equatorial Pacific
attribute NC_GLOBAL projects_0_name String Gene content, gene expression, and physiology in mesopelagic ammonia-oxidizing archaea
attribute NC_GLOBAL projects_0_project_nid String 555307
attribute NC_GLOBAL projects_0_start_date String 2013-04
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 Organism,Tax_ID
attribute NC_GLOBAL summary String Nitrosopelagicus brevis CN25 and U25 were grown in nitrogen replete and deplete conditions, with subsequent transcriptome sequencing.
attribute NC_GLOBAL title String [Thaumarchaea transcriptomes] - Nitrosopelagicus brevis CN25 and U25 grown in nitrogen replete and deplete conditions, with subsequent transcriptome sequencing and identification. (Gene content, gene expression, and physiology in mesopelagic ammonia-oxidizing archaea)
attribute NC_GLOBAL version String 1
attribute NC_GLOBAL xml_source String osprey2erddap.update_xml() v1.3
variable Accession String
attribute Accession bcodmo_name String accession number
attribute Accession description String Accession number and NCBI link
attribute Accession long_name String Accession
attribute Accession units String unitless
variable Sample_Name String
attribute Sample_Name bcodmo_name String sample
attribute Sample_Name description String Sample name
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 Organism String
attribute Organism bcodmo_name String species
attribute Organism description String Species of organism
attribute Organism long_name String Organism
attribute Organism units String unitless
variable Tax_ID int
attribute Tax_ID _FillValue int 2147483647
attribute Tax_ID actual_range int 1410606, 1410606
attribute Tax_ID bcodmo_name String sample
attribute Tax_ID description String Taxonomic identification
attribute Tax_ID long_name String Tax ID
attribute Tax_ID nerc_identifier String https://vocab.nerc.ac.uk/collection/P02/current/ACYC/ (external link)
attribute Tax_ID units String unitless
variable Strain String
attribute Strain bcodmo_name String sample
attribute Strain description String Strain identification
attribute Strain long_name String Strain
attribute Strain nerc_identifier String https://vocab.nerc.ac.uk/collection/P02/current/ACYC/ (external link)
attribute Strain units String unitless

 
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