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 Published methodology in Landa et al., 2017, ISME Journal, in press.\n \nOne liter samples were filtered through 2-um polycarbonate (PC) membranes to\ncollect bacterial cells and flash-frozen in liquid nitrogen and stored at\n-80C. Filters were extracted for RNA by the acid\nphenol:chloroform:isoamylalcohol method. Potential traces of DNA were removed\nusing the Turbo DNA-free kit (Invitrogen, Waltham, MA, USA). Samples were\ntested for residual DNA by a 40-cycle PCR targeting the 16S rRNA gene of R.\npomeroyi. Samples were depleted of rRNA using custom probes for small and\nlarge subunit rRNA genes from all three microbes (Stewart et al., 2010).\nLibraries were prepared for two replicate cubitainers at 8 time points (16\nsamples) using the KAPA Stranded mRNA-Seq Kit (Kapa Biosystems, Wilmington,\nMA, USA) at the Georgia Genomics Facility (University of Georgia) and\nsequenced on a HiSeq Illumina 2500 at the Hudson Alpha Institute for\nBiotechnology (AL, USA).\n \nReference cited:  \n Stewart FJ, Ottesen EA, DeLong EF. (2010). Development and quantitative\nanalyses of a universal rRNA-subtraction protocol for microbial\nmetatranscriptomics. ISME J 4: 896\\u2013907.\ndoi:[10.1038/ismej.2010.18](\\\\\"https://dx.doi.org/10.1038/ismej.2010.18\\\\\")
attribute NC_GLOBAL awards_0_award_nid String 541254
attribute NC_GLOBAL awards_0_award_number String OCE-1342694
attribute NC_GLOBAL awards_0_data_url String http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1342694 (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 Switch RNAseq Data \n PI: Mary Ann Moran (University of Georgia) \n Version: 29 November 2017 \n Note: Transcript counts are reported in TPM (transcripts per million). This is the number of transcript \n       reads mapped to an individual gene for every million transcripts mapped to the entire genome.
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 2017-11-27T20:45:13Z
attribute NC_GLOBAL date_modified String 2020-01-14T16:35:14Z
attribute NC_GLOBAL defaultDataQuery String &time<now
attribute NC_GLOBAL doi String 10.1575/1912/bco-dmo.719970.1
attribute NC_GLOBAL infoUrl String https://www.bco-dmo.org/dataset/719970 (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 Transcripts were sequenced on a HiSeq Illumina 2500 at the Hudson Alpha Institute for Biotechnology (AL, USA).
attribute NC_GLOBAL instruments_0_dataset_instrument_nid String 720063
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 bco, bco-dmo, biological, chemical, data, dataset, day12, Day12_R1, Day12_R2, day15, Day15_R1, Day15_R2, day18, Day18_R1, Day18_R2, day23, Day23_R1, Day23_R2, day30, Day30_R1, Day30_R2, day37, Day37_R1, Day37_R2, day7, Day7_R1, Day7_R2, day9, Day9_R1, Day9_R2, description, dmo, erddap, locus, Locus_Tag, management, oceanography, office, preliminary, tag
attribute NC_GLOBAL license String https://www.bco-dmo.org/dataset/719970/license (external link)
attribute NC_GLOBAL metadata_source String https://www.bco-dmo.org/api/dataset/719970 (external link)
attribute NC_GLOBAL param_mapping String {'719970': {}}
attribute NC_GLOBAL parameter_source String https://www.bco-dmo.org/mapserver/dataset/719970/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 Shannon Rauch
attribute NC_GLOBAL people_1_person_nid String 51498
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 OceanSulfurFluxBact
attribute NC_GLOBAL projects_0_acronym String OceanSulfurFluxBact
attribute NC_GLOBAL projects_0_description String Surface ocean bacterioplankton preside over a divergence point in the marine sulfur cycle where the fate of dimethylsulfoniopropionate (DMSP) is determined. While it is well recognized that this juncture influences the fate of sulfur in the ocean and atmosphere, its regulation by bacterioplankton is not yet understood. Based on recent findings in biogeochemistry, bacterial physiology, bacterial genetics, and ocean instrumentation, the microbial oceanography community is poised to make major advances in knowledge of this control point. This research project is ascertaining how the major taxa of bacterial DMSP degraders in seawater regulate DMSP transformations, and addresses the implications of bacterial functional, genetic, and taxonomic diversity for global sulfur cycling.\nThe project is founded on the globally important function of bacterial transformation of the ubiquitous organic sulfur compound DMSP in ocean surface waters. Recent genetic discoveries have identified key genes in the two major DMSP degradation pathways, and the stage is now set to identify the factors that regulate gene expression to favor one or the other pathway during DMSP processing. The taxonomy of the bacteria mediating DMSP cycling has been deduced from genomic and metagenomic sequencing surveys to include four major groups of surface ocean bacterioplankton. How regulation of DMSP degradation differs among these groups and maps to phylogeny in co-occurring members is key information for understanding the marine sulfur cycle and predicting its function in a changing ocean. Using model organism studies, microcosm experiments (at Dauphin Island Sea Lab, AL), and time-series field studies with an autonomous sample collection instrument (at Monterey Bay, CA), this project is taking a taxon-specific approach to decipher the regulation of bacterial DMSP degradation.\nThis research addresses fundamental questions of how the diversity of microbial life influences the geochemical environment of the oceans and atmosphere, linking the genetic basis of metabolic potential to taxonomic diversity. The project is training graduate students and post-doctoral scholars in microbial biodiversity and providing research opportunities and mentoring for undergraduate students. An outreach program is enhance understanding of the role and diversity of marine microorganisms in global elemental cycles among high school students. Advanced Placement Biology students are participating in marine microbial research that covers key learning goals in the AP Biology curriculum. Two high school students are selected each year for summer research internships in PI laboratories.
attribute NC_GLOBAL projects_0_end_date String 2018-12
attribute NC_GLOBAL projects_0_name String Bacterial Taxa that Control Sulfur Flux from the Ocean to the Atmosphere
attribute NC_GLOBAL projects_0_project_nid String 541255
attribute NC_GLOBAL projects_0_start_date String 2014-01
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 summary String Transcriptional profile of marine bacterium Ruegeria pomeroyi in a three-member co-culture study. This dataset contains the processed, QC'ed, normalized sequence data. The full raw data file is deposited in the NCBI BioProject database under accession PRJNA381627.
attribute NC_GLOBAL title String [Switch RNAseq] - Transcriptional profile of marine bacterium Ruegeria pomeroyi in a three-member co-culture study (Bacterial Taxa that Control Sulfur Flux from the Ocean to the Atmosphere)
attribute NC_GLOBAL version String 1
attribute NC_GLOBAL xml_source String osprey2erddap.update_xml() v1.3
variable Locus_Tag String
attribute Locus_Tag bcodmo_name String sample
attribute Locus_Tag description String gene identifier
attribute Locus_Tag long_name String Locus Tag
attribute Locus_Tag nerc_identifier String https://vocab.nerc.ac.uk/collection/P02/current/ACYC/ (external link)
attribute Locus_Tag units String unitless
variable Description String
attribute Description bcodmo_name String brief_desc
attribute Description description String gene function, if known
attribute Description long_name String Description
attribute Description units String unitless
variable Day7_R1 String
attribute Day7_R1 bcodmo_name String count
attribute Day7_R1 description String Transcript count by day and replicate: day 7, replicate 1
attribute Day7_R1 long_name String Day7 R1
attribute Day7_R1 units String TPM (transcripts per million)
variable Day7_R2 String
attribute Day7_R2 bcodmo_name String count
attribute Day7_R2 description String Transcript count by day and replicate: day 7, replicate 2
attribute Day7_R2 long_name String Day7 R2
attribute Day7_R2 units String TPM (transcripts per million)
variable Day9_R1 String
attribute Day9_R1 bcodmo_name String count
attribute Day9_R1 description String Transcript count by day and replicate: day 9, replicate 1
attribute Day9_R1 long_name String Day9 R1
attribute Day9_R1 units String TPM (transcripts per million)
variable Day9_R2 String
attribute Day9_R2 bcodmo_name String count
attribute Day9_R2 description String Transcript count by day and replicate: day 9, replicate 2
attribute Day9_R2 long_name String Day9 R2
attribute Day9_R2 units String TPM (transcripts per million)
variable Day12_R1 String
attribute Day12_R1 bcodmo_name String count
attribute Day12_R1 description String Transcript count by day and replicate: day 12, replicate 1
attribute Day12_R1 long_name String Day12 R1
attribute Day12_R1 units String TPM (transcripts per million)
variable Day12_R2 String
attribute Day12_R2 bcodmo_name String count
attribute Day12_R2 description String Transcript count by day and replicate: day 12, replicate 2
attribute Day12_R2 long_name String Day12 R2
attribute Day12_R2 units String TPM (transcripts per million)
variable Day15_R1 String
attribute Day15_R1 bcodmo_name String count
attribute Day15_R1 description String Transcript count by day and replicate: day 15, replicate 1
attribute Day15_R1 long_name String Day15 R1
attribute Day15_R1 units String TPM (transcripts per million)
variable Day15_R2 String
attribute Day15_R2 bcodmo_name String count
attribute Day15_R2 description String Transcript count by day and replicate: day 15, replicate 2
attribute Day15_R2 long_name String Day15 R2
attribute Day15_R2 units String TPM (transcripts per million)
variable Day18_R1 String
attribute Day18_R1 bcodmo_name String count
attribute Day18_R1 description String Transcript count by day and replicate: day 18, replicate 1
attribute Day18_R1 long_name String Day18 R1
attribute Day18_R1 units String TPM (transcripts per million)
variable Day18_R2 String
attribute Day18_R2 bcodmo_name String count
attribute Day18_R2 description String Transcript count by day and replicate: day 18, replicate 2
attribute Day18_R2 long_name String Day18 R2
attribute Day18_R2 units String TPM (transcripts per million)
variable Day23_R1 String
attribute Day23_R1 bcodmo_name String count
attribute Day23_R1 description String Transcript count by day and replicate: day 23, replicate 1
attribute Day23_R1 long_name String Day23 R1
attribute Day23_R1 units String TPM (transcripts per million)
variable Day23_R2 String
attribute Day23_R2 bcodmo_name String count
attribute Day23_R2 description String Transcript count by day and replicate: day 23, replicate 2
attribute Day23_R2 long_name String Day23 R2
attribute Day23_R2 units String TPM (transcripts per million)
variable Day30_R1 String
attribute Day30_R1 bcodmo_name String count
attribute Day30_R1 description String Transcript count by day and replicate: day 30, replicate 1
attribute Day30_R1 long_name String Day30 R1
attribute Day30_R1 units String TPM (transcripts per million)
variable Day30_R2 String
attribute Day30_R2 bcodmo_name String count
attribute Day30_R2 description String Transcript count by day and replicate: day 30, replicate 2
attribute Day30_R2 long_name String Day30 R2
attribute Day30_R2 units String TPM (transcripts per million)
variable Day37_R1 String
attribute Day37_R1 bcodmo_name String count
attribute Day37_R1 description String Transcript count by day and replicate: day 37, replicate 1
attribute Day37_R1 long_name String Day37 R1
attribute Day37_R1 units String TPM (transcripts per million)
variable Day37_R2 String
attribute Day37_R2 bcodmo_name String count
attribute Day37_R2 description String Transcript count by day and replicate: day 37, replicate 2
attribute Day37_R2 long_name String Day37 R2
attribute Day37_R2 units String TPM (transcripts per million)

 
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