Accessing BCO-DMO data
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BCO-DMO ERDDAP
Accessing BCO-DMO data |
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| Dataset Title: | [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) 
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| Institution: | BCO-DMO (Dataset ID: bcodmo_dataset_739636) |
| Information: | Summary
| License
| ISO 19115
| Metadata
| Background
| Subset
| Files
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Attributes {
s {
Accession {
String bcodmo_name "accession number";
String description "Accession number and NCBI link";
String long_name "Accession";
String units "unitless";
}
Sample_Name {
String bcodmo_name "sample";
String description "Sample name";
String long_name "Sample Name";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P02/current/ACYC/";
String units "unitless";
}
Organism {
String bcodmo_name "species";
String description "Species of organism";
String long_name "Organism";
String units "unitless";
}
Tax_ID {
Int32 _FillValue 2147483647;
Int32 actual_range 1410606, 1410606;
String bcodmo_name "sample";
String description "Taxonomic identification";
String long_name "Tax ID";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P02/current/ACYC/";
String units "unitless";
}
Strain {
String bcodmo_name "sample";
String description "Strain identification";
String long_name "Strain";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P02/current/ACYC/";
String units "unitless";
}
}
NC_GLOBAL {
String access_formats ".htmlTable,.csv,.json,.mat,.nc,.tsv";
String acquisition_description "Thaumarchaea transcriptomes sequences.";
String awards_0_award_nid "555306";
String awards_0_award_number "OCE-1259994";
String awards_0_data_url "http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1259994";
String awards_0_funder_name "NSF Division of Ocean Sciences";
String awards_0_funding_acronym "NSF OCE";
String awards_0_funding_source_nid "355";
String awards_0_program_manager "David L. Garrison";
String awards_0_program_manager_nid "50534";
String awards_1_award_nid "555311";
String awards_1_award_number "OCE-1260006";
String awards_1_data_url "http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1260006";
String awards_1_funder_name "NSF Division of Ocean Sciences";
String awards_1_funding_acronym "NSF OCE";
String awards_1_funding_source_nid "355";
String awards_1_program_manager "David L. Garrison";
String awards_1_program_manager_nid "50534";
String cdm_data_type "Other";
String comment
"Thaumarchaea transcriptomes
C. Dupont & A. Santoro, PIs
Version 10 July 2018";
String Conventions "COARDS, CF-1.6, ACDD-1.3";
String creator_email "info@bco-dmo.org";
String creator_name "BCO-DMO";
String creator_type "institution";
String creator_url "https://www.bco-dmo.org/";
String data_source "extract_data_as_tsv version 2.3 19 Dec 2019";
String date_created "2018-07-10T18:08:40Z";
String date_modified "2019-06-12T13:34:50Z";
String defaultDataQuery "&time<now";
String doi "10.1575/1912/bco-dmo.739636.1";
String history
"2024-12-22T12:02:11Z (local files)
2024-12-22T12:02:11Z https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_739636.html";
String infoUrl "https://www.bco-dmo.org/dataset/739636";
String institution "BCO-DMO";
String instruments_0_acronym "Automated Sequencer";
String instruments_0_dataset_instrument_description "Used to identify samples";
String instruments_0_dataset_instrument_nid "739746";
String instruments_0_description "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.";
String instruments_0_instrument_name "Automated DNA Sequencer";
String instruments_0_instrument_nid "649";
String instruments_0_supplied_name "Illumina NextSEQ 500";
String keywords "accession, bco, bco-dmo, biological, chemical, data, dataset, dmo, erddap, management, name, oceanography, office, organism, preliminary, sample, Sample_Name, strain, tax, Tax_ID";
String license "https://www.bco-dmo.org/dataset/739636/license";
String metadata_source "https://www.bco-dmo.org/api/dataset/739636";
String param_mapping "{'739636': {}}";
String parameter_source "https://www.bco-dmo.org/mapserver/dataset/739636/parameters";
String people_0_affiliation "J. Craig Venter Institute";
String people_0_affiliation_acronym "JCVI";
String people_0_person_name "Christopher Dupont";
String people_0_person_nid "555309";
String people_0_role "Principal Investigator";
String people_0_role_type "originator";
String people_1_affiliation "University of California-Santa Barbara";
String people_1_affiliation_acronym "UCSB";
String people_1_person_name "Alyson Santoro";
String people_1_person_nid "555313";
String people_1_role "Co-Principal Investigator";
String people_1_role_type "originator";
String people_2_affiliation "J. Craig Venter Institute";
String people_2_affiliation_acronym "JCVI";
String people_2_person_name "Christopher Dupont";
String people_2_person_nid "555309";
String people_2_role "Contact";
String people_2_role_type "related";
String people_3_affiliation "Woods Hole Oceanographic Institution";
String people_3_affiliation_acronym "WHOI BCO-DMO";
String people_3_person_name "Hannah Ake";
String people_3_person_nid "650173";
String people_3_role "BCO-DMO Data Manager";
String people_3_role_type "related";
String project "AmoA Archaea";
String projects_0_acronym "AmoA Archaea";
String projects_0_description
"NSF award abstract:
Intellectual 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:
1. 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
2. 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
The 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.
Broader 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.";
String projects_0_end_date "2018-03";
String projects_0_geolocation "Epipelagic and mesopelagic, Equatorial Pacific";
String projects_0_name "Gene content, gene expression, and physiology in mesopelagic ammonia-oxidizing archaea";
String projects_0_project_nid "555307";
String projects_0_start_date "2013-04";
String publisher_name "Biological and Chemical Oceanographic Data Management Office (BCO-DMO)";
String publisher_type "institution";
String sourceUrl "(local files)";
String standard_name_vocabulary "CF Standard Name Table v55";
String subsetVariables "Organism,Tax_ID";
String summary "Nitrosopelagicus brevis CN25 and U25 were grown in nitrogen replete and deplete conditions, with subsequent transcriptome sequencing.";
String title "[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)";
String version "1";
String xml_source "osprey2erddap.update_xml() v1.3";
}
}
Data Access Protocol (DAP) and its
selection constraints.
The URL specifies what you want: the dataset, a description of the graph or the subset of the data, and the file type for the response.
Tabledap request URLs must be in the form
https://coastwatch.pfeg.noaa.gov/erddap/tabledap/datasetID.fileType{?query}
For example,
https://coastwatch.pfeg.noaa.gov/erddap/tabledap/pmelTaoDySst.htmlTable?longitude,latitude,time,station,wmo_platform_code,T_25&time>=2015-05-23T12:00:00Z&time<=2015-05-31T12:00:00Z
Thus, the query is often a comma-separated list of desired variable names,
followed by a collection of
constraints (e.g., variable<value),
each preceded by '&' (which is interpreted as "AND").
For details, see the tabledap Documentation.