Accessing BCO-DMO data
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BCO-DMO ERDDAP
Accessing BCO-DMO data |
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| Dataset Title: | [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) 
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| Institution: | BCO-DMO (Dataset ID: bcodmo_dataset_746654) |
| Information: | Summary
| License
| ISO 19115
| Metadata
| Background
| Subset
| Files
| Make a graph
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Attributes {
s {
bioproject_accession {
String bcodmo_name "accession number";
String description "collection of biological data related to a single initiative";
String long_name "Bioproject Accession";
String units "unitless";
}
biosample_accession {
String bcodmo_name "accession number";
String description "code for accessing short read sequence data from NCBI";
String long_name "Biosample Accession";
String units "unitless";
}
library_ID {
String bcodmo_name "sample";
String description "sample name code";
String long_name "Library ID";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P02/current/ACYC/";
String units "unitless";
}
title {
String bcodmo_name "sample_descrip";
String description "description and type of the sample";
String long_name "Title";
String units "unitless";
}
library_strategy {
String bcodmo_name "unknown";
String description "type of sequencing performed to generate the sample";
String long_name "Library Strategy";
String units "unitless";
}
library_source {
String bcodmo_name "unknown";
String description "type of sequence data represented by the sample";
String long_name "Library Source";
String units "unitless";
}
library_selection {
String bcodmo_name "unknown";
String description "how reads were prescreened (unspecified indicates reads were not screened)";
String long_name "Library Selection";
String units "unitless";
}
library_layout {
String bcodmo_name "unknown";
String description "whether sequenced reads were single or paired-end";
String long_name "Library Layout";
String units "unitless";
}
platform {
String bcodmo_name "instrument";
String description "sequencing machine platform used to generate reads";
String long_name "Platform";
String units "unitless";
}
instrument_model {
String bcodmo_name "instrument";
String description "make and model of the sequencing machine platform used";
String long_name "Instrument Model";
String units "unitless";
}
design_description {
String bcodmo_name "unknown";
String description "quick methods description detailing how genetic material was prepared prior to sequencing";
String long_name "Design Description";
String units "unitless";
}
filetype {
String bcodmo_name "unknown";
String description "type of file the reads are stored as";
String long_name "Filetype";
String units "unitless";
}
assembly {
Float64 _FillValue NaN;
String bcodmo_name "unknown";
String description "whether or not there is a linked assembly (blank indicates that no assembly is provided)";
String long_name "Assembly";
String units "unitless";
}
filename {
String bcodmo_name "file_name";
String description "name of the first read file";
String long_name "Filename";
String units "unitless";
}
filename2 {
String bcodmo_name "file_name";
String description "name of the second read file";
String long_name "Filename2";
String units "unitless";
}
filename3 {
String bcodmo_name "file_name";
String description "name of the third read file";
String long_name "Filename3";
String units "unitless";
}
filename4 {
String bcodmo_name "file_name";
String description "name of the fourth read file";
String long_name "Filename4";
String units "unitless";
}
filename5 {
Float64 _FillValue NaN;
String bcodmo_name "file_name";
String description "additional read file (if present)";
String long_name "Filename5";
String units "unitless";
}
filename6 {
Float64 _FillValue NaN;
String bcodmo_name "file_name";
String description "additional read file (if present)";
String long_name "Filename6";
String units "unitless";
}
filename7 {
Float64 _FillValue NaN;
String bcodmo_name "file_name";
String description "additional read file (if present)";
String long_name "Filename7";
String units "unitless";
}
filename8 {
Float64 _FillValue NaN;
String bcodmo_name "file_name";
String description "additional read file (if present)";
String long_name "Filename8";
String units "unitless";
}
}
NC_GLOBAL {
String access_formats ".htmlTable,.csv,.json,.mat,.nc,.tsv";
String acquisition_description
"Samples were collected on cruise AE1409.\\u00a0Trichodesmium colonies were
obtained by net tow (130 micron mesh) and serially washed in sterile surface
seawater. Clean colonies were then incubated with or without a cocktail of
quorum sensing molecules. After four hours of incubation, colonies were placed
onto filters and stored in liquid nitrogen until RNA was extracted and
submitted for sequencing at the Columbia University Genome Center.\\u00a0
Methods:\\u00a0We extracted prokaryotic RNA from triplicate control and +AHL
samples by first adding approximately 500 \\u03bcL of glass beads to each
cryotube and bead beating with a vortex adaptor for 5 minutes. We extracted
total RNA using the yeast protocol from the Qiagen RNeasy Mini Kit with the
added on-column DNase digestion using the RNase-free DNase Kit (Qiagen,
Hilden, Germany). We processed DNase-treated total RNA through a MICROBEnrich
kit following the manufacturer\\u2019s instructions (ThermoFisher Scientific,
Waltham, MA, USA). We removed ribosomal RNA using a Ribo-Zero Magnetic Kit
optimized for bacteria (Illumina, San Diego, CA, USA) following the
manufacturer\\u2019s instructions. Finally, we purified the prokaryotic RNA
extract using the RNeasy MinElute Cleanup Kit by following manufacturer
instructions and eluting in 14 \\u03bcL water (Qiagen). We pooled together
triplicate samples, and pooled RNA extracts were quantified using the Take3
Nucleic Acid Quantification program and a Biotek plate reader. To further
assess quality of pooled triplicate RNA samples, we used a BioAnalyzer and the
RNA 6000 Nano Kit (Agilent Technologies, Santa Clara, CA, USA). The JP
Sulzberger Genome Center at Columbia University carried out RNA sequencing
with a depth of 60 million paired end reads using an Illumina HiSeq protocol.
Quality control:\\u00a0We trimmed sequence reads and normalized following the
Eel Pond Protocol for mRNAseq assembly. To obtain read counts for each sample,
we mapped cleaned forward and reverse reads to metagenome assemblies from the
same sampling locations that were previously characterized and clustered into
orthologous groups (OGs). We carried out mapping using RSEM with the paired-
end and Bowtie2 parameters. We summed counts for previously determined OGs for
Trichodesmium and epibiont genome bins separately. We determined significant
changes in OG relative abundance between control and +AHL samples by comparing
control and sample treatments using a stringent empirical Bayes approach
called Analysis of Sequence Counts (ASC). This approach evaluates the
posterior probability associated with a given fold change across pooled
triplicates, and performs similarly, but conservatively, on replicated and
unreplicated sample datasets. \\u00a0OGs were considered significantly higher
or lower if they had a 95% or higher posterior probability of a fold change
greater than 2 between treatment and control. Taxonomic relative abundance
estimates for metagenome samples were previously calculated by multiplying the
length of each contig in a genome bin by read mapping coverage, and then
summing those values for all contigs. Please refer to the manuscript related
to this metadata for more details and references.";
String awards_0_award_nid "565175";
String awards_0_award_number "OCE-1332898";
String awards_0_data_url "http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1332898";
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 "Donald L. Rice";
String awards_0_program_manager_nid "51467";
String awards_1_award_nid "565184";
String awards_1_award_number "OCE-1332912";
String awards_1_data_url "http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1332912";
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 "Donald L. Rice";
String awards_1_program_manager_nid "51467";
String cdm_data_type "Other";
String comment
"Trichodesmium AHL metatranscriptome accessions
Alantic Explorer AE1409, PABST cruise, May 2014
S. Dyhrman (LDEO), B. Van Mooy (WHOI), K. Frischkorn (LDEO)
version: 2018-09-21
Link to NCBI BioProject PRJNA450995: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA450995";
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 "2018-09-21T20:13:26Z";
String date_modified "2019-03-20T14:30:43Z";
String defaultDataQuery "&time<now";
String doi "10.1575/1912/bco-dmo.746654.1";
String history
"2024-11-21T15:52:33Z (local files)
2024-11-21T15:52:33Z https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_746654.html";
String infoUrl "https://www.bco-dmo.org/dataset/746654";
String institution "BCO-DMO";
String instruments_0_acronym "Plankton Net";
String instruments_0_dataset_instrument_description "The net had 130 micron mesh and was used to collect Trichodesmium colonies.";
String instruments_0_dataset_instrument_nid "746665";
String instruments_0_description "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.";
String instruments_0_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L05/current/22/";
String instruments_0_instrument_name "Plankton Net";
String instruments_0_instrument_nid "525";
String instruments_0_supplied_name "net";
String instruments_1_acronym "Automated Sequencer";
String instruments_1_dataset_instrument_nid "746667";
String instruments_1_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_1_instrument_name "Automated DNA Sequencer";
String instruments_1_instrument_nid "649";
String instruments_1_supplied_name "Illumina Miseq platform";
String instruments_2_acronym "Thermal Cycler";
String instruments_2_dataset_instrument_nid "746666";
String instruments_2_description
"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.
(adapted from http://serc.carleton.edu/microbelife/research_methods/genomics/pcr.html)";
String instruments_2_instrument_name "PCR Thermal Cycler";
String instruments_2_instrument_nid "471582";
String keywords "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";
String license "https://www.bco-dmo.org/dataset/746654/license";
String metadata_source "https://www.bco-dmo.org/api/dataset/746654";
String param_mapping "{'746654': {}}";
String parameter_source "https://www.bco-dmo.org/mapserver/dataset/746654/parameters";
String people_0_affiliation "Lamont-Doherty Earth Observatory";
String people_0_affiliation_acronym "LDEO";
String people_0_person_name "Sonya T. Dyhrman";
String people_0_person_nid "51101";
String people_0_role "Principal Investigator";
String people_0_role_type "originator";
String people_1_affiliation "Woods Hole Oceanographic Institution";
String people_1_affiliation_acronym "WHOI";
String people_1_person_name "Benjamin A.S. Van Mooy";
String people_1_person_nid "50975";
String people_1_role "Co-Principal Investigator";
String people_1_role_type "originator";
String people_2_affiliation "Lamont-Doherty Earth Observatory";
String people_2_affiliation_acronym "LDEO";
String people_2_person_name "Kyle R. Frischkorn";
String people_2_person_nid "746669";
String people_2_role "Student";
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 "Nancy Copley";
String people_3_person_nid "50396";
String people_3_role "BCO-DMO Data Manager";
String people_3_role_type "related";
String project "P Processing by Tricho";
String projects_0_acronym "P Processing by Tricho";
String projects_0_description
"Description from NSF award abstract:
Colonies 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.
In 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.";
String projects_0_end_date "2016-09";
String projects_0_geolocation "Western Tropical North Atlantic";
String projects_0_name "Dissolved Phosphorus Processing by Trichodesmium Consortia: Quantitative Partitioning, Role of Microbial Coordination, and Impact on Nitrogen Fixation";
String projects_0_project_nid "565176";
String projects_0_start_date "2013-10";
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 "bioproject_accession,library_strategy,library_source,library_selection,library_layout,platform,instrument_model,design_description,filetype,assembly,filename5,filename6,filename7,filename8";
String summary "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.";
String title "[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)";
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.