http://lod.bco-dmo.org/id/dataset/746654
eng; USA
utf8
dataset
Highest level of data collection, from a common set of sensors or instrumentation, usually within the same research project
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
2018-09-21
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Trichodesmium AHL amendment metatranscriptomic reads accessions and metadata
2018-09-21
publication
2018-09-21
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2019-04-01
publication
https://doi.org/10.1575/1912/bco-dmo.746654.1
Sonya T. Dyhrman
Lamont-Doherty Earth Observatory
principalInvestigator
Benjamin A.S. Van Mooy
Woods Hole Oceanographic Institution
principalInvestigator
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
publisher
Cite this dataset as: Dyhrman, S., Van Mooy, B. (2018) Trichodesmium AHL amendment metatranscriptomic reads accessions and metadata. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2018-09-21 [if applicable, indicate subset used]. doi:10.1575/1912/bco-dmo.746654.1 [access date]
GenBank Trichodesmium accessions and associated metadata Dataset Description: <p>The samples are composed of raw metatranscriptomic reads from acyl homoserine lactone (AHL) (quorum sensing) addition incubation experiments performed on Trichodesmium colonies collected in May 2014 on the 'PABST' cruise (R/V Atlantic Explorer AE1409) in the Sargasso Sea. We extracted prokaryotic RNA from triplicate control and +AHL samples, pooling together triplicate samples and sequencing 60 million paired end reads.</p>
<p>Links to the NCBI GenBank BioProjects are provided.</p>
<p>Raw reads can also be found on the NCBI SRA under accession code <a href="http://www.ncbi.nlm.nih.gov/bioproject/PRJNA330995" target="_blank">PRJNA450995</a>.</p> Methods and Sampling: <p>Samples were collected on cruise AE1409.&nbsp;Trichodesmium 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.&nbsp;</p>
<p>Methods:&nbsp;We extracted prokaryotic RNA from triplicate control and +AHL samples by first adding approximately 500 μL 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’s 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’s instructions. Finally, we purified the prokaryotic RNA extract using the RNeasy MinElute Cleanup Kit by following manufacturer instructions and eluting in 14 μL 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.</p>
<p>Quality control:&nbsp;We 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. &nbsp;OGs 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.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1332898 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1332898
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1332912 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1332912
completed
Sonya T. Dyhrman
Lamont-Doherty Earth Observatory
845-365-8465
102E Geoscience 61 Route 9W, PO Box 1000
Palisades
NY
10964
USA
dyhrman@ldeo.columbia.edu
pointOfContact
Benjamin A.S. Van Mooy
Woods Hole Oceanographic Institution
(508) 289 2322
Department of Marine Chemistry and Geochemistry, MS #4, Fye 117 Woods Hole Oceanographic Institution
Woods Hole
MA
02543
USA
bvanmooy@whoi.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
bioproject_accession
biosample_accession
library_ID
title
library_strategy
library_source
library_selection
library_layout
platform
instrument_model
design_description
filetype
assembly
filename
filename2
filename3
filename4
filename5
filename6
filename7
filename8
Illumina Miseq platform
net
theme
None, User defined
accession number
sample identification
sample description
No BCO-DMO term
instrument
file_name
featureType
BCO-DMO Standard Parameters
Automated DNA Sequencer
Plankton Net
Thermal Cycler
instrument
BCO-DMO Standard Instruments
AE1409
service
Deployment Activity
Western Tropical North Atlantic
place
Locations
otherRestrictions
otherRestrictions
Access Constraints: none. Use Constraints: Please follow guidelines at: http://www.bco-dmo.org/terms-use Distribution liability: Under no circumstances shall BCO-DMO be liable for any direct, incidental, special, consequential, indirect, or punitive damages that result from the use of, or the inability to use, the materials in this data submission. If you are dissatisfied with any materials in this data submission your sole and exclusive remedy is to discontinue use.
Dissolved Phosphorus Processing by Trichodesmium Consortia: Quantitative Partitioning, Role of Microbial Coordination, and Impact on Nitrogen Fixation
https://osprey.bco-dmo.org/project/565176
Dissolved Phosphorus Processing by Trichodesmium Consortia: Quantitative Partitioning, Role of Microbial Coordination, and Impact on Nitrogen Fixation
<p><em>Description from NSF award abstract:</em><br />
Colonies of the cyanbacterium <em>Trichodesmium</em> are responsible for a large fraction of N2 fixation in nutrient-poor, open-ocean ecosystems, ultimately fueling primary production in both <em>Trichodesmium</em> and in the broader planktonic community. However, in some parts of the ocean, the scarcity of dissolved phosphorus limits rates of <em>Trichodesmium </em>N2 fixation. <em>Trichodesmium</em> 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.</p>
<p>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 <em>Trichodesmium </em>consortia, and to discern the role of quorum sensing in phosphorus acquisition and partitioning. Results from this study are expected to expand understanding of <em>Trichodesmium</em> 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.</p>
P Processing by Tricho
largerWorkCitation
project
eng; USA
biota
oceans
Western Tropical North Atlantic
-64.9988
-52.1795
7.4618
30.4177
2014-05-08
2014-05-26
Western Tropical North Atlantic
0
BCO-DMO catalogue of parameters from Trichodesmium AHL amendment metatranscriptomic reads accessions and metadata
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
http://lod.bco-dmo.org/id/dataset-parameter/747747.rdf
Name: bioproject_accession
Units: unitless
Description: <p>collection of biological data related to a single initiative</p>
http://lod.bco-dmo.org/id/dataset-parameter/747748.rdf
Name: biosample_accession
Units: unitless
Description: <p>code for accessing short read sequence data from NCBI</p>
http://lod.bco-dmo.org/id/dataset-parameter/747749.rdf
Name: library_ID
Units: unitless
Description: <p>sample name code</p>
http://lod.bco-dmo.org/id/dataset-parameter/747750.rdf
Name: title
Units: unitless
Description: <p>description and type of the sample</p>
http://lod.bco-dmo.org/id/dataset-parameter/747751.rdf
Name: library_strategy
Units: unitless
Description: <p>type of sequencing performed to generate the sample</p>
http://lod.bco-dmo.org/id/dataset-parameter/747752.rdf
Name: library_source
Units: unitless
Description: <p>type of sequence data represented by the sample</p>
http://lod.bco-dmo.org/id/dataset-parameter/747753.rdf
Name: library_selection
Units: unitless
Description: <p>how reads were prescreened (unspecified indicates reads were not screened)</p>
http://lod.bco-dmo.org/id/dataset-parameter/747754.rdf
Name: library_layout
Units: unitless
Description: <p>whether sequenced reads were single or paired-end</p>
http://lod.bco-dmo.org/id/dataset-parameter/747755.rdf
Name: platform
Units: unitless
Description: <p>sequencing machine platform used to generate reads</p>
http://lod.bco-dmo.org/id/dataset-parameter/747756.rdf
Name: instrument_model
Units: unitless
Description: <p>make and model of the sequencing machine platform used</p>
http://lod.bco-dmo.org/id/dataset-parameter/747757.rdf
Name: design_description
Units: unitless
Description: <p>quick methods description detailing how genetic material was prepared prior to sequencing</p>
http://lod.bco-dmo.org/id/dataset-parameter/747758.rdf
Name: filetype
Units: unitless
Description: <p>type of file the reads are stored as</p>
http://lod.bco-dmo.org/id/dataset-parameter/747759.rdf
Name: assembly
Units: unitless
Description: <p>whether or not there is a linked assembly (blank indicates that no assembly is provided)</p>
http://lod.bco-dmo.org/id/dataset-parameter/747760.rdf
Name: filename
Units: unitless
Description: <p>name of the first read file</p>
http://lod.bco-dmo.org/id/dataset-parameter/747761.rdf
Name: filename2
Units: unitless
Description: <p>name of the second read file</p>
http://lod.bco-dmo.org/id/dataset-parameter/747762.rdf
Name: filename3
Units: unitless
Description: <p>name of the third read file</p>
http://lod.bco-dmo.org/id/dataset-parameter/747763.rdf
Name: filename4
Units: unitless
Description: <p>name of the fourth read file</p>
http://lod.bco-dmo.org/id/dataset-parameter/747764.rdf
Name: filename5
Units: unitless
Description: <p>additional read file (if present)</p>
http://lod.bco-dmo.org/id/dataset-parameter/747765.rdf
Name: filename6
Units: unitless
Description: <p>additional read file (if present)</p>
http://lod.bco-dmo.org/id/dataset-parameter/747766.rdf
Name: filename7
Units: unitless
Description: <p>additional read file (if present)</p>
http://lod.bco-dmo.org/id/dataset-parameter/747767.rdf
Name: filename8
Units: unitless
Description: <p>additional read file (if present)</p>
GB/NERC/BODC > British Oceanographic Data Centre, Natural Environment Research Council, United Kingdom
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
2627
https://darchive.mblwhoilibrary.org/bitstream/1912/23943/1/dataset-746654_trichodesmium-ahl-metatranscriptomesae1409__v1.tsv
download
https://doi.org/10.1575/1912/bco-dmo.746654.1
download
onLine
dataset
<p>Samples were collected on cruise AE1409.&nbsp;Trichodesmium 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.&nbsp;</p>
<p>Methods:&nbsp;We extracted prokaryotic RNA from triplicate control and +AHL samples by first adding approximately 500 μL 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’s 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’s instructions. Finally, we purified the prokaryotic RNA extract using the RNeasy MinElute Cleanup Kit by following manufacturer instructions and eluting in 14 μL 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.</p>
<p>Quality control:&nbsp;We 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. &nbsp;OGs 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.</p>
Specified by the Principal Investigator(s)
<p><strong>BCO-DMO Processing: (to be edited)</strong><br />
Added conventional header with dataset name, PI name, version date.<br />
Modified parameter names to conform with BCO-DMO naming conventions.</p>
Specified by the Principal Investigator(s)
asNeeded
7.x-1.1
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
Illumina Miseq platform
Illumina Miseq platform
PI Supplied Instrument Name: Illumina Miseq platform Instrument Name: Automated DNA Sequencer Instrument Short Name:Automated Sequencer Instrument Description: A DNA sequencer is an instrument that determines the order of deoxynucleotides in deoxyribonucleic acid sequences.
net
net
PI Supplied Instrument Name: net PI Supplied Instrument Description:The net had 130 micron mesh and was used to collect Trichodesmium colonies. Instrument Name: Plankton Net Instrument Short Name:Plankton Net Instrument 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. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/22/
PI Supplied Instrument Name: Instrument Name: Thermal Cycler Instrument Short Name:Thermal Cycler Instrument Description: A thermal cycler or "thermocycler" is a general term for a type of laboratory apparatus, commonly used for performing polymerase chain reaction (PCR), that is capable of repeatedly altering and maintaining specific temperatures for defined periods of time. 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. They can also be used to facilitate other temperature-sensitive reactions, including restriction enzyme digestion or rapid diagnostics.
(adapted from http://serc.carleton.edu/microbelife/research_methods/genomics/pcr.html)
Cruise: AE1409
AE1409
R/V Atlantic Explorer
Community Standard Description
International Council for the Exploration of the Sea
R/V Atlantic Explorer
vessel
AE1409
Benjamin A.S. Van Mooy
Woods Hole Oceanographic Institution
R/V Atlantic Explorer
Community Standard Description
International Council for the Exploration of the Sea
R/V Atlantic Explorer
vessel