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 Samples were collected on cruise AE1409.\\u00a0Trichodesmium colonies were\nobtained by net tow (130 micron mesh) and serially washed in sterile surface\nseawater. Clean colonies were then incubated with or without a cocktail of\nquorum sensing molecules. After four hours of incubation, colonies were placed\nonto filters and stored in liquid nitrogen until RNA was extracted and\nsubmitted for sequencing at the Columbia University Genome Center.\\u00a0\n \nMethods:\\u00a0We extracted prokaryotic RNA from triplicate control and +AHL\nsamples by first adding approximately 500 \\u03bcL of glass beads to each\ncryotube and bead beating with a vortex adaptor for 5 minutes. We extracted\ntotal RNA using the yeast protocol from the Qiagen RNeasy Mini Kit with the\nadded on-column DNase digestion using the RNase-free DNase Kit (Qiagen,\nHilden, Germany). We processed DNase-treated total RNA through a MICROBEnrich\nkit following the manufacturer\\u2019s instructions (ThermoFisher Scientific,\nWaltham, MA, USA). We removed ribosomal RNA using a Ribo-Zero Magnetic Kit\noptimized for bacteria (Illumina, San Diego, CA, USA) following the\nmanufacturer\\u2019s instructions. Finally, we purified the prokaryotic RNA\nextract using the RNeasy MinElute Cleanup Kit by following manufacturer\ninstructions and eluting in 14 \\u03bcL water (Qiagen). We pooled together\ntriplicate samples, and pooled RNA extracts were quantified using the Take3\nNucleic Acid Quantification program and a Biotek plate reader. To further\nassess quality of pooled triplicate RNA samples, we used a BioAnalyzer and the\nRNA 6000 Nano Kit (Agilent Technologies, Santa Clara, CA, USA). The JP\nSulzberger Genome Center at Columbia University carried out RNA sequencing\nwith a depth of 60 million paired end reads using an Illumina HiSeq protocol.\n \nQuality control:\\u00a0We trimmed sequence reads and normalized following the\nEel Pond Protocol for mRNAseq assembly. To obtain read counts for each sample,\nwe mapped cleaned forward and reverse reads to metagenome assemblies from the\nsame sampling locations that were previously characterized and clustered into\northologous groups (OGs). We carried out mapping using RSEM with the paired-\nend and Bowtie2 parameters. We summed counts for previously determined OGs for\nTrichodesmium and epibiont genome bins separately. We determined significant\nchanges in OG relative abundance between control and +AHL samples by comparing\ncontrol and sample treatments using a stringent empirical Bayes approach\ncalled Analysis of Sequence Counts (ASC). This approach evaluates the\nposterior probability associated with a given fold change across pooled\ntriplicates, and performs similarly, but conservatively, on replicated and\nunreplicated sample datasets. \\u00a0OGs were considered significantly higher\nor lower if they had a 95% or higher posterior probability of a fold change\ngreater than 2 between treatment and control. Taxonomic relative abundance\nestimates for metagenome samples were previously calculated by multiplying the\nlength of each contig in a genome bin by read mapping coverage, and then\nsumming those values for all contigs. Please refer to the manuscript related\nto this metadata for more details and references.
attribute NC_GLOBAL awards_0_award_nid String 565175
attribute NC_GLOBAL awards_0_award_number String OCE-1332898
attribute NC_GLOBAL awards_0_data_url String http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1332898 (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 Donald L. Rice
attribute NC_GLOBAL awards_0_program_manager_nid String 51467
attribute NC_GLOBAL awards_1_award_nid String 565184
attribute NC_GLOBAL awards_1_award_number String OCE-1332912
attribute NC_GLOBAL awards_1_data_url String http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1332912 (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 Donald L. Rice
attribute NC_GLOBAL awards_1_program_manager_nid String 51467
attribute NC_GLOBAL cdm_data_type String Other
attribute NC_GLOBAL comment String Trichodesmium AHL metatranscriptome accessions \n   Alantic Explorer AE1409, PABST cruise, May 2014 \n   S. Dyhrman (LDEO), B. Van Mooy (WHOI), K. Frischkorn (LDEO) \n   version: 2018-09-21 \n    Link to NCBI BioProject PRJNA450995: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA450995
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 2018-09-21T20:13:26Z
attribute NC_GLOBAL date_modified String 2019-03-20T14:30:43Z
attribute NC_GLOBAL defaultDataQuery String &time<now
attribute NC_GLOBAL doi String 10.1575/1912/bco-dmo.746654.1
attribute NC_GLOBAL infoUrl String https://www.bco-dmo.org/dataset/746654 (external link)
attribute NC_GLOBAL institution String BCO-DMO
attribute NC_GLOBAL instruments_0_acronym String Plankton Net
attribute NC_GLOBAL instruments_0_dataset_instrument_description String The net had 130 micron mesh and was used to collect Trichodesmium colonies.
attribute NC_GLOBAL instruments_0_dataset_instrument_nid String 746665
attribute NC_GLOBAL instruments_0_description String A Plankton Net is a generic term for a sampling net that is used to collect plankton. It is used only when detailed instrument documentation is not available.
attribute NC_GLOBAL instruments_0_instrument_external_identifier String https://vocab.nerc.ac.uk/collection/L05/current/22/ (external link)
attribute NC_GLOBAL instruments_0_instrument_name String Plankton Net
attribute NC_GLOBAL instruments_0_instrument_nid String 525
attribute NC_GLOBAL instruments_0_supplied_name String net
attribute NC_GLOBAL instruments_1_acronym String Automated Sequencer
attribute NC_GLOBAL instruments_1_dataset_instrument_nid String 746667
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 Illumina Miseq platform
attribute NC_GLOBAL instruments_2_acronym String Thermal Cycler
attribute NC_GLOBAL instruments_2_dataset_instrument_nid String 746666
attribute NC_GLOBAL instruments_2_description String General term for a laboratory apparatus commonly used for performing polymerase chain reaction (PCR). The device has a thermal block with holes where tubes with the PCR reaction mixtures can be inserted. The cycler then raises and lowers the temperature of the block in discrete, pre-programmed steps.\n\n(adapted from http://serc.carleton.edu/microbelife/research_methods/genomics/pcr.html)
attribute NC_GLOBAL instruments_2_instrument_name String PCR Thermal Cycler
attribute NC_GLOBAL instruments_2_instrument_nid String 471582
attribute NC_GLOBAL keywords String accession, assembly, bco, bco-dmo, biological, bioproject, bioproject_accession, biosample, biosample_accession, chemical, data, dataset, description, design, design_description, dmo, erddap, filename, filename2, filename3, filename4, filename5, filename6, filename7, filename8, filetype, instrument, instrument_model, layout, library, library_ID, library_layout, library_selection, library_source, library_strategy, management, model, oceanography, office, platform, preliminary, selection, source, strategy, title
attribute NC_GLOBAL license String https://www.bco-dmo.org/dataset/746654/license (external link)
attribute NC_GLOBAL metadata_source String https://www.bco-dmo.org/api/dataset/746654 (external link)
attribute NC_GLOBAL param_mapping String {'746654': {}}
attribute NC_GLOBAL parameter_source String https://www.bco-dmo.org/mapserver/dataset/746654/parameters (external link)
attribute NC_GLOBAL people_0_affiliation String Lamont-Doherty Earth Observatory
attribute NC_GLOBAL people_0_affiliation_acronym String LDEO
attribute NC_GLOBAL people_0_person_name String Sonya T. Dyhrman
attribute NC_GLOBAL people_0_person_nid String 51101
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
attribute NC_GLOBAL people_1_person_name String Benjamin A.S. Van Mooy
attribute NC_GLOBAL people_1_person_nid String 50975
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 Lamont-Doherty Earth Observatory
attribute NC_GLOBAL people_2_affiliation_acronym String LDEO
attribute NC_GLOBAL people_2_person_name String Kyle R. Frischkorn
attribute NC_GLOBAL people_2_person_nid String 746669
attribute NC_GLOBAL people_2_role String Student
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 Nancy Copley
attribute NC_GLOBAL people_3_person_nid String 50396
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 P Processing by Tricho
attribute NC_GLOBAL projects_0_acronym String P Processing by Tricho
attribute NC_GLOBAL projects_0_description String Description from NSF award abstract:\nColonies of the cyanbacterium Trichodesmium are responsible for a large fraction of N2 fixation in nutrient-poor, open-ocean ecosystems, ultimately fueling primary production in both Trichodesmium and in the broader planktonic community. However, in some parts of the ocean, the scarcity of dissolved phosphorus limits rates of Trichodesmium N2 fixation. Trichodesmium colonies employ an arsenal of strategies to mitigate the effects of phosphorus limitation, and the consortia of epibiotic bacteria in the colonies may play a significant role in phosphorus acquisition.\nIn this study, researchers from Woods Hole Oceanographic Institution and Columbia University will use metagenomic and metatranscriptomic sequencing to investigate how phosphorus metabolism is coordinated in Trichodesmium consortia, and to discern the role of quorum sensing in phosphorus acquisition and partitioning. Results from this study are expected to expand understanding of Trichodesmium from a monospecific colony whose primary function is fixing CO2 and N2 toward a unique planktonic consortium with a diverse, complex, and highly coordinated overall metabolism that exerts profound control over the cycling of inorganic and organic nutrients in the oligotrophic upper ocean.
attribute NC_GLOBAL projects_0_end_date String 2016-09
attribute NC_GLOBAL projects_0_geolocation String Western Tropical North Atlantic
attribute NC_GLOBAL projects_0_name String Dissolved Phosphorus Processing by Trichodesmium Consortia: Quantitative Partitioning, Role of Microbial Coordination, and Impact on Nitrogen Fixation
attribute NC_GLOBAL projects_0_project_nid String 565176
attribute NC_GLOBAL projects_0_start_date String 2013-10
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 bioproject_accession,library_strategy,library_source,library_selection,library_layout,platform,instrument_model,design_description,filetype,assembly,filename5,filename6,filename7,filename8
attribute NC_GLOBAL summary String Trichodesmium is a marine, diazotrophic cyanobacterium that plays a central role in the biogeochemical cycling of carbon and nitrogen. Colonies ubiquitously co-occur with a diverse microbiome of heterotrophic bacteria. Here we show that manipulation of the microbiome with quorum sensing acyl homoserine lactone (AHL) molecules significantly modulated rates of N2 fixation by Trichodesmium collected from the western North Atlantic, with both positive and negative effects of varied magnitude. Changes in Trichodesmium N2 fixation did not clearly correlate with changes in microbiome composition or geochemical patterns. Metatranscriptome sequencing revealed significant changes in the relative abundance of microbiome transcripts encoding metabolic functions consistent with quorum sensing responses in model bacteria. There was little overlap in specific microbiome transcriptional responses to AHL addition between stations, and this variability in microbiome gene expression may underpin the heterogeneous changes in Trichodesmium N2 fixation. These data suggest the microbiome could play a large and previously overlooked role in modulating Trichodesmium N2 fixation. This metadata form describes the metatranscriptomic sequencing reads that were used in the study.
attribute NC_GLOBAL title String [Trichodesmium AHL metatranscriptomes_AE1409] - Trichodesmium AHL amendment metatranscriptomic reads accessions and metadata (Dissolved Phosphorus Processing by Trichodesmium Consortia: Quantitative Partitioning, Role of Microbial Coordination, and Impact on Nitrogen Fixation)
attribute NC_GLOBAL version String 1
attribute NC_GLOBAL xml_source String osprey2erddap.update_xml() v1.3
variable bioproject_accession String
attribute bioproject_accession bcodmo_name String accession number
attribute bioproject_accession description String collection of biological data related to a single initiative
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 code for accessing short read sequence data from 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
attribute library_ID description String sample name code
attribute library_ID long_name String Library ID
attribute library_ID nerc_identifier String https://vocab.nerc.ac.uk/collection/P02/current/ACYC/ (external link)
attribute library_ID units String unitless
variable title String
attribute title bcodmo_name String sample_descrip
attribute title description String description and type of the sample
attribute title long_name String Title
attribute title units String unitless
variable library_strategy String
attribute library_strategy bcodmo_name String unknown
attribute library_strategy description String type of sequencing performed to generate the sample
attribute library_strategy long_name String Library Strategy
attribute library_strategy units String unitless
variable library_source String
attribute library_source bcodmo_name String unknown
attribute library_source description String type of sequence data represented by the sample
attribute library_source long_name String Library Source
attribute library_source units String unitless
variable library_selection String
attribute library_selection bcodmo_name String unknown
attribute library_selection description String how reads were prescreened (unspecified indicates reads were not screened)
attribute library_selection long_name String Library Selection
attribute library_selection units String unitless
variable library_layout String
attribute library_layout bcodmo_name String unknown
attribute library_layout description String whether sequenced reads were single or paired-end
attribute library_layout long_name String Library Layout
attribute library_layout units String unitless
variable platform String
attribute platform bcodmo_name String instrument
attribute platform description String sequencing machine platform used to generate reads
attribute platform long_name String Platform
attribute platform units String unitless
variable instrument_model String
attribute instrument_model bcodmo_name String instrument
attribute instrument_model description String make and model of the sequencing machine platform used
attribute instrument_model long_name String Instrument Model
attribute instrument_model units String unitless
variable design_description String
attribute design_description bcodmo_name String unknown
attribute design_description description String quick methods description detailing how genetic material was prepared prior to sequencing
attribute design_description long_name String Design Description
attribute design_description units String unitless
variable filetype String
attribute filetype bcodmo_name String unknown
attribute filetype description String type of file the reads are stored as
attribute filetype long_name String Filetype
attribute filetype units String unitless
variable assembly double
attribute assembly _FillValue double NaN
attribute assembly bcodmo_name String unknown
attribute assembly description String whether or not there is a linked assembly (blank indicates that no assembly is provided)
attribute assembly long_name String Assembly
attribute assembly units String unitless
variable filename String
attribute filename bcodmo_name String file_name
attribute filename description String name of the first read file
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 the second read file
attribute filename2 long_name String Filename2
attribute filename2 units String unitless
variable filename3 String
attribute filename3 bcodmo_name String file_name
attribute filename3 description String name of the third read file
attribute filename3 long_name String Filename3
attribute filename3 units String unitless
variable filename4 String
attribute filename4 bcodmo_name String file_name
attribute filename4 description String name of the fourth read file
attribute filename4 long_name String Filename4
attribute filename4 units String unitless
variable filename5 double
attribute filename5 _FillValue double NaN
attribute filename5 bcodmo_name String file_name
attribute filename5 description String additional read file (if present)
attribute filename5 long_name String Filename5
attribute filename5 units String unitless
variable filename6 double
attribute filename6 _FillValue double NaN
attribute filename6 bcodmo_name String file_name
attribute filename6 description String additional read file (if present)
attribute filename6 long_name String Filename6
attribute filename6 units String unitless
variable filename7 double
attribute filename7 _FillValue double NaN
attribute filename7 bcodmo_name String file_name
attribute filename7 description String additional read file (if present)
attribute filename7 long_name String Filename7
attribute filename7 units String unitless
variable filename8 double
attribute filename8 _FillValue double NaN
attribute filename8 bcodmo_name String file_name
attribute filename8 description String additional read file (if present)
attribute filename8 long_name String Filename8
attribute filename8 units String unitless

 
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