BCO-DMO ERDDAP
Accessing BCO-DMO data 		log in    
Brought to you by BCO-DMO    
 
 
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 Thalassiosira pseudonana were removed from the co-cultures by pre-filtration\nthrough 2.0 \\u00b5m pore-size filters, and bacteria were collected on 0.2\n\\u00b5m pore-size filters. Filters were incubated in SDS (0.6% final\nconcentration) and proteinase K (120 ng \\u03bcl \\u20131 final concentration).\nRNA was extracted from duplicates of each treatment by adding an equal volume\nof acid phenol:chloroform:isoamyl-alcohol, followed by shaking,\ncentrifugation, and collection of the supernatant. A second extraction was\ncarried out by the addition of an equal volume of chloroform:isoamyl-alcohol.\nRNA was recovered from the supernatant, treated to remove rRNA, and sequenced.\n \nEach sequence library is from four independent bacterial samples that were\npooled for sequencing. The data are assigned to one of the four samples post-\nsequencing by mapping to the genomes of each of the four bacteria. The data\ntable provides the accession numbers of the bacterial genomes to be used for\nmapping in the final column.
attribute NC_GLOBAL awards_0_award_nid String 765520
attribute NC_GLOBAL awards_0_award_number String IOS-1656311
attribute NC_GLOBAL awards_0_data_url String http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1656311 (external link)
attribute NC_GLOBAL awards_0_funder_name String NSF Division of Integrative Organismal Systems
attribute NC_GLOBAL awards_0_funding_acronym String NSF IOS
attribute NC_GLOBAL awards_0_funding_source_nid String 626136
attribute NC_GLOBAL awards_0_program_manager String Mamta Rawat
attribute NC_GLOBAL awards_0_program_manager_nid String 765519
attribute NC_GLOBAL cdm_data_type String Other
attribute NC_GLOBAL comment String Diatom Matrix RNAseq \n     NCBI accessions for transcriptome data for bacteria collected 8 hrs after individual inoculation into a diatom Thalassiosira psuedonana culture. \n   PI: M. A. Moran (UGA) \n   version date: 2020-07-16
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 2020-07-16T14:58:37Z
attribute NC_GLOBAL date_modified String 2020-07-20T20:17:45Z
attribute NC_GLOBAL defaultDataQuery String &time<now
attribute NC_GLOBAL doi String 10.26008/1912/bco-dmo.818765.1
attribute NC_GLOBAL infoUrl String https://www.bco-dmo.org/dataset/818765 (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_nid String 818797
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 HiSeq Illumina 2500
attribute NC_GLOBAL keywords String accession, bco, bco-dmo, bio, biological, bioproject, BioSample, chemical, data, dataset, description, dmo, erddap, genome, management, microbe, name, ncbi, NCBI_Bioproject_Accession, NCBI_Genome_Accession, oceanography, office, preliminary, replicate, sample, Sample_Name, taxon, taxon_microbe
attribute NC_GLOBAL license String https://www.bco-dmo.org/dataset/818765/license (external link)
attribute NC_GLOBAL metadata_source String https://www.bco-dmo.org/api/dataset/818765 (external link)
attribute NC_GLOBAL param_mapping String {'818765': {}}
attribute NC_GLOBAL parameter_source String https://www.bco-dmo.org/mapserver/dataset/818765/parameters (external link)
attribute NC_GLOBAL people_0_affiliation String University of Georgia
attribute NC_GLOBAL people_0_affiliation_acronym String UGA
attribute NC_GLOBAL people_0_person_name String Mary Ann Moran
attribute NC_GLOBAL people_0_person_nid String 51592
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 Woods Hole Oceanographic Institution
attribute NC_GLOBAL people_1_affiliation_acronym String WHOI BCO-DMO
attribute NC_GLOBAL people_1_person_name String Nancy Copley
attribute NC_GLOBAL people_1_person_nid String 50396
attribute NC_GLOBAL people_1_role String BCO-DMO Data Manager
attribute NC_GLOBAL people_1_role_type String related
attribute NC_GLOBAL project String Metabolic Currencies
attribute NC_GLOBAL projects_0_acronym String Metabolic Currencies
attribute NC_GLOBAL projects_0_description String NSF Award Abstract:\nThe roles of microbes in cycling carbon and nutrients in the ocean - the largest biological system on Earth - were initially described about 40 years ago. Now, it is known that half of Earth's primary production is carried out by marine phytoplankton, and half of that is recycled within weeks by marine bacteria. This proposal is a collaboration between microbiologists and chemists to identify the specific compounds that pass between phytoplankton and bacteria in surface ocean waters. Identifying the key chemicals of the ocean's microbial food web will provide insights into how the marine carbon cycle is regulated, generate data to improve ocean carbon models, and train new scientists at the interface of microbiology and chemistry. Hands-on learning opportunities in microbial ecology will be provided for high school students, both in the classroom and in marine ecosystems of the Georgia coast.\nPhytoplankton metabolites that sustain the flow of carbon between microbial autotrophs and heterotrophs in the surface ocean carbon cycle will be identified in this project. A matrix of model systems consisting of bacteria-phytoplankton co-cultures will be used as biological assays for key metabolites based on expression patterns of bacterial transporter genes. The chemical identity of candidate metabolites and evaluation of their potential ecological role will be carried out by exometabolomic analysis of co-cultures with bacterial transporter mutants. Both advanced mass spectrometry and NMR will be used for metabolomics analysis, taking advantage of the sensitivity and compound identification strengths of each. The distribution of candidate metabolites in the ocean microbiome and other microbial systems will be characterized by mining environmental sequence datasets for orthologous transporter genes. This project represents a novel approach to identifying metabolites important in microbiome function, compounds often difficult to address with standard chemical approaches because of their low concentrations and high biological demand.
attribute NC_GLOBAL projects_0_end_date String 2020-06
attribute NC_GLOBAL projects_0_name String Metabolic Currencies of the Ocean Carbon Cycle
attribute NC_GLOBAL projects_0_project_nid String 765521
attribute NC_GLOBAL projects_0_start_date String 2017-07
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 standard_name_vocabulary String CF Standard Name Table v55
attribute NC_GLOBAL subsetVariables String NCBI_Bioproject_Accession
attribute NC_GLOBAL summary String Transcriptome data for bacteria Ruegeria pomeroyi DSS-3, Stenotrophomonas sp. SKA14, Polaribacter dokdonensis MED152, and Dokdonia MED134 collected eight hours after individual inoculation into a diatom Thalassiosira psuedonana culture. The sequence data description for PRHNA448168 is at https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA448168.
attribute NC_GLOBAL title String [Diatom Matrix RNAseq] - Transcriptome data for bacteria collected eight hours after individual inoculation into a diatom Thalassiosira psuedonana culture (Metabolic Currencies of the Ocean Carbon Cycle)
attribute NC_GLOBAL version String 1
attribute NC_GLOBAL xml_source String osprey2erddap.update_xml() v1.5
variable Sample_Name String
attribute Sample_Name bcodmo_name String sample
attribute Sample_Name description String sample identifier
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 NCBI_Bioproject_Accession String
attribute NCBI_Bioproject_Accession bcodmo_name String accession number
attribute NCBI_Bioproject_Accession description String NCBI Bioproject accession number
attribute NCBI_Bioproject_Accession long_name String NCBI Bioproject Accession
attribute NCBI_Bioproject_Accession units String unitless
variable BioSample String
attribute BioSample bcodmo_name String accession number
attribute BioSample description String NCBI Biosample accession number
attribute BioSample long_name String Bio Sample
attribute BioSample units String unitless
variable Description String
attribute Description bcodmo_name String sample_descrip
attribute Description description String Description of sample
attribute Description long_name String Description
attribute Description units String unitless
variable replicate byte
attribute replicate _FillValue byte 127
attribute replicate actual_range byte 1, 2
attribute replicate bcodmo_name String replicate
attribute replicate description String Replicate number
attribute replicate long_name String Replicate
attribute replicate units String unitless
variable NCBI_Genome_Accession String
attribute NCBI_Genome_Accession bcodmo_name String accession number
attribute NCBI_Genome_Accession description String NCBI Genome accession number
attribute NCBI_Genome_Accession long_name String NCBI Genome Accession
attribute NCBI_Genome_Accession units String unitless
variable taxon_microbe String
attribute taxon_microbe bcodmo_name String taxon
attribute taxon_microbe description String Microbial identification
attribute taxon_microbe long_name String Taxon Microbe
attribute taxon_microbe units String unitless

 
ERDDAP, Version 2.22
Disclaimers | Privacy Policy | Contact