http://lod.bco-dmo.org/id/dataset/626776
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
2015-11-20
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
NCBI accession numbers for metagenomic sequences collected from the R/V JOIDES Resolution (JRES-204) cruise in the Cascadia Continental Margin during 2002 (Methane-Hydrate Sediment Omics project)
2015-12-02
publication
2015-12-02
revision
BCO-DMO Linked Data URI
2015-12-02
creation
http://lod.bco-dmo.org/id/dataset/626776
Jennifer B. Glass
Georgia Institute of Technology
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: Glass, J. B. (2015) NCBI accession numbers for metagenomic sequences collected from the R/V JOIDES Resolution (JRES-204) cruise in the Cascadia Continental Margin during 2002 (Methane-Hydrate Sediment Omics project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 2015-12-02) Version Date 2015-12-02 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/626776 [access date]
NCBI accession numbers for metagenomic sequences: IODP Site 1244, Hydrate Ridge, offshore Oregon Dataset Description: <p>This dataset was generated under a C-DEBI research grant.</p>
<p><strong>Related References:</strong></p>
<p>Tréhu, A.M, Bohrmann, G., Rack, F.R., Torres, M.E., et al., 2003. Proc. ODP, Init. Repts., 204: College Station, TX (Ocean Drilling Program).doi:10.2973/odp.proc.ir.204.2003</p>
<p>Shipboard Scientific Party, 2003. Site 1244. In Tréhu, A.M, Bohrmann, G., Rack, F.R., Torres, M.E., et al., Proc. ODP, Init. Repts., 204: College Station, TX (Ocean Drilling Program), 1–132. doi:10.2973/odp.proc.ir.204.103.2003</p>
<p>Tréhu, A.M., Bohrmann, G., Torres, M.E., and Colwell, F.S. (Eds.), 2006. Proc. ODP, Sci. Results, 204: College Station, TX (Ocean Drilling Program).doi:10.2973/odp.proc.sr.204.2006</p> Methods and Sampling: <p><strong>DNA extraction and purification</strong></p>
<p>DNA was extracted, in duplicate, from 8 to 20 g of of “Mobio” IODP sediment samples previously frozen at -80C&nbsp; using a Powersoil total RNA Isolation Kit&nbsp;with the DNA Elution Accessory Kit (MO-BIO Laboratories, Solana Beach, CA, USA) following the manufacturer protocol but without beads. Approximately 2 grams of sediments were utilized for each extraction, and DNA pellets from each depth were pooled together. DNA concentrations were measured using a Qubit 2.0 fluorometer with dsDNA High Sensitivity reagents (Invitrogen, Grand Island, NY, USA). The DNA from the extractions that yielded robust 16S rRNA and metagenomic sequences ranged from 3.75-15 ng of DNA per gram of sediments.</p>
<p><strong>Multiple Displacement Amplification (MDA)</strong></p>
<p>DNA was amplified using a REPLI-g Single Cell Kit (Qiagen, Germantown, MD, USA). Tubes, tube caps and reverse transcription-PCR grade water (Ambion, Grand Island, NY, USA) were UV-treated for 15 min in a PCR laminar flow hood. Quantitative PCR showed that the negative control began amplifying after 5 hr of incubation at 30°C, and therefore, the 30°C incubation step was shortened to 5 hr using a Bio-Rad C1000 Touch thermal cycler (Bio-Rad, Hercules, CA, USA). DNA concentrations were measured in duplicate on a Qubit 2.0 with dsDNA High Sensitivity reagents (Invitrogen, Grand Island, NY, USA).</p>
<p><strong>Illumina library preparation and sequencing</strong></p>
<p>Two micrograms of MDA DNA were used to generate genome libraries using a TruSeq DNA PCR-Free Kit following the manufacturer’s protocol (Illumina, San Diego, CA, USA). The resulting libraries were sequenced using a Rapid-Run on an Illumina HiSeq 2500 (Center for Integrative Genomics, Georgia Institute of Technology) to obtain 100 bp paired-end reads</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-0939564 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=0939564
completed
Jennifer B. Glass
Georgia Institute of Technology
404-894-3942
School of Earth & Atmospheric Sciences
Atlanta
GA
30332
USA
jennifer.glass@eas.gatech.edu
pointOfContact
asNeeded
Dataset Version: 2015-12-02
Unknown
cruise_id
site
lat
lon
BioSample
sample
SRA
NCBI_accession
theme
None, User defined
Cruise identfier
site
latitude
longitude
No BCO-DMO term
sample identification
featureType
BCO-DMO Standard Parameters
Automated DNA Sequencer
Thermal Cycler
instrument
BCO-DMO Standard Instruments
JRES-204
service
Deployment Activity
Cascadia Continental Margin
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.
Center for Dark Energy Biosphere Investigations
http://www.darkenergybiosphere.org
Center for Dark Energy Biosphere Investigations
The mission of the Center for Dark Energy Biosphere Investigations (C-DEBI) is to explore life beneath the seafloor and make transformative discoveries that advance science, benefit society, and inspire people of all ages and origins.
C-DEBI provides a framework for a large, multi-disciplinary group of scientists to pursue fundamental questions about life deep in the sub-surface environment of Earth. The fundamental science questions of C-DEBI involve exploration and discovery, uncovering the processes that constrain the sub-surface biosphere below the oceans, and implications to the Earth system. What type of life exists in this deep biosphere, how much, and how is it distributed and dispersed? What are the physical-chemical conditions that promote or limit life? What are the important oxidation-reduction processes and are they unique or important to humankind? How does this biosphere influence global energy and material cycles, particularly the carbon cycle? Finally, can we discern how such life evolved in geological settings beneath the ocean floor, and how this might relate to ideas about the origin of life on our planet?
C-DEBI's scientific goals are pursued with a combination of approaches:
(1) coordinate, integrate, support, and extend the research associated with four major programs—Juan de Fuca Ridge flank (JdF), South Pacific Gyre (SPG), North Pond (NP), and Dorado Outcrop (DO)—and other field sites;
(2) make substantial investments of resources to support field, laboratory, analytical, and modeling studies of the deep subseafloor ecosystems;
(3) facilitate and encourage synthesis and thematic understanding of submarine microbiological processes, through funding of scientific and technical activities, coordination and hosting of meetings and workshops, and support of (mostly junior) researchers and graduate students; and
(4) entrain, educate, inspire, and mentor an interdisciplinary community of researchers and educators, with an emphasis on undergraduate and graduate students and early-career scientists.
Note: Katrina Edwards was a former PI of C-DEBI; James Cowen is a former co-PI.
Data Management:
C-DEBI is committed to ensuring all the data generated are publically available and deposited in a data repository for long-term storage as stated in their Data Management Plan (PDF) and in compliance with the NSF Ocean Sciences Sample and Data Policy. The data types and products resulting from C-DEBI-supported research include a wide variety of geophysical, geological, geochemical, and biological information, in addition to education and outreach materials, technical documents, and samples. All data and information generated by C-DEBI-supported research projects are required to be made publically available either following publication of research results or within two (2) years of data generation.
To ensure preservation and dissemination of the diverse data-types generated, C-DEBI researchers are working with BCO-DMO Data Managers make data publicly available online. The partnership with BCO-DMO helps ensure that the C-DEBI data are discoverable and available for reuse. Some C-DEBI data is better served by specialized repositories (NCBI's GenBank for sequence data, for example) and, in those cases, BCO-DMO provides dataset documentation (metadata) that includes links to those external repositories.
C-DEBI
largerWorkCitation
program
International Ocean Discovery Program
http://www.iodp.org/index.php
International Ocean Discovery Program
The International Ocean Discovery Program (IODP) is an international marine research collaboration that explores Earth's history and dynamics using ocean-going research platforms to recover data recorded in seafloor sediments and rocks and to monitor subseafloor environments. IODP depends on facilities funded by three platform providers with financial contributions from five additional partner agencies. Together, these entities represent 26 nations whose scientists are selected to staff IODP research expeditions conducted throughout the world's oceans.
IODP expeditions are developed from hypothesis-driven science proposals aligned with the program's science plan Illuminating Earth's Past, Present, and Future. The science plan identifies 14 challenge questions in the four areas of climate change, deep life, planetary dynamics, and geohazards.
IODP's three platform providers include:
The U.S. National Science Foundation (NSF)
Japan's Ministry of Education, Culture, Sports, Science and Technology (MEXT)
The European Consortium for Ocean Research Drilling (ECORD)
More information on IODP, including the Science Plan and Policies/Procedures, can be found on their website at http://www.iodp.org/program-documents.
A summary table with links to IODP datasets currently hosted on Zenodo (https://zenodo.org/communities/iodp) can be accessed using the following link: https://iodp.tamu.edu/database/zenodo.html
IODP
largerWorkCitation
program
Functional gene diversity and expression in methane-hydrate bearing deep subsurface sediments
https://osprey.bco-dmo.org/project/626690
Functional gene diversity and expression in methane-hydrate bearing deep subsurface sediments
<p>Methane is a critical component of the deep subsurface. In shallow marine sediments, anaerobic oxidation of methane (AOM) is coupled to sulfate reduction. However, relatively little is known about which microbial metabolisms are active in deeply buried sediment containing methane hydrates, particularly with regard to alternative electron acceptors that could fuel deep AOM. We propose to determine which microbial population(s) and functional genes are active in the deep biosphere beneath Hydrate Ridge offshore Oregon by sequencing metagenomes and metatranscriptomes from samples drilled on ODP Leg 204 and archived for future molecular analysis. We will analyze gene diversity and expression in six geochemically distinct zones from 2 to 139 meters below the seafloor with the goal of evaluating the relationship between geochemical conditions (i.e. sulfate, iron and manganese availability) and microbial metabolic activity.</p>
<p><strong>Related References:</strong></p>
<p>Tréhu, A.M, Bohrmann, G., Rack, F.R., Torres, M.E., et al., 2003. Proc. ODP, Init. Repts., 204: College Station, TX (Ocean Drilling Program).<a href="http://dx.doi.org/10.2973/odp.proc.ir.204.2003" target="_blank">doi:10.2973/odp.proc.ir.204.2003</a></p>
<p>Shipboard Scientific Party, 2003. Site 1244. In Tréhu, A.M, Bohrmann, G., Rack, F.R., Torres, M.E., et al., Proc. ODP, Init. Repts., 204: College Station, TX (Ocean Drilling Program), 1–132. <a href="http://dx.doi.org/10.2973/odp.proc.ir.204.103.2003" target="_blank">doi:10.2973/odp.proc.ir.204.103.2003</a></p>
<p>Tréhu, A.M., Bohrmann, G., Torres, M.E., and Colwell, F.S. (Eds.), 2006. Proc. ODP, Sci. Results, 204: College Station, TX (Ocean Drilling Program).<a href="http://dx.doi.org/10.2973/odp.proc.sr.204.2006" target="_blank"> doi:10.2973/odp.proc.sr.204.2006</a></p>
<p>---</p>
<p>This work was supported by a C-DEBI Research Grant.</p>
Methane-Hydrate Sediment Omics
largerWorkCitation
project
eng; USA
biota
oceans
Cascadia Continental Margin
2015-12-02
Hydrate Ridge, North Pacific, offshore Oregon
0
BCO-DMO catalogue of parameters from NCBI accession numbers for metagenomic sequences collected from the R/V JOIDES Resolution (JRES-204) cruise in the Cascadia Continental Margin during 2002 (Methane-Hydrate Sediment Omics 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
http://lod.bco-dmo.org/id/dataset-parameter/626838.rdf
Name: cruise_id
Units: unitless
Description: <p>cruise identification</p>
http://lod.bco-dmo.org/id/dataset-parameter/626839.rdf
Name: site
Units: unitless
Description: <p>site identification</p>
http://lod.bco-dmo.org/id/dataset-parameter/626840.rdf
Name: lat
Units: decimal degrees
Description: <p>latitude; north is positive</p>
http://lod.bco-dmo.org/id/dataset-parameter/626841.rdf
Name: lon
Units: decimal degrees
Description: <p>longitude; east is positive</p>
http://lod.bco-dmo.org/id/dataset-parameter/626842.rdf
Name: BioSample
Units: unitless
Description: <p>NCBI BioSample id</p>
http://lod.bco-dmo.org/id/dataset-parameter/626843.rdf
Name: sample
Units: unitless
Description: <p>sample identification</p>
http://lod.bco-dmo.org/id/dataset-parameter/626844.rdf
Name: SRA
Units: unitless
Description: <p>NCBI SRA (Sequence Read Archive) id</p>
http://lod.bco-dmo.org/id/dataset-parameter/626845.rdf
Name: NCBI_accession
Units: unitless
Description: <p>NCBI accession number with link</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
2287
https://datadocs.bco-dmo.org/file/GwwAkGxfOkODgG/metagenome_accessions.csv
metagenome_accessions.csv
Primary data file for dataset ID 626776
download
https://osprey.bco-dmo.org/dataset/626776/data/download
download
onLine
dataset
<p><strong>DNA extraction and purification</strong></p>
<p>DNA was extracted, in duplicate, from 8 to 20 g of of “Mobio” IODP sediment samples previously frozen at -80C&nbsp; using a Powersoil total RNA Isolation Kit&nbsp;with the DNA Elution Accessory Kit (MO-BIO Laboratories, Solana Beach, CA, USA) following the manufacturer protocol but without beads. Approximately 2 grams of sediments were utilized for each extraction, and DNA pellets from each depth were pooled together. DNA concentrations were measured using a Qubit 2.0 fluorometer with dsDNA High Sensitivity reagents (Invitrogen, Grand Island, NY, USA). The DNA from the extractions that yielded robust 16S rRNA and metagenomic sequences ranged from 3.75-15 ng of DNA per gram of sediments.</p>
<p><strong>Multiple Displacement Amplification (MDA)</strong></p>
<p>DNA was amplified using a REPLI-g Single Cell Kit (Qiagen, Germantown, MD, USA). Tubes, tube caps and reverse transcription-PCR grade water (Ambion, Grand Island, NY, USA) were UV-treated for 15 min in a PCR laminar flow hood. Quantitative PCR showed that the negative control began amplifying after 5 hr of incubation at 30°C, and therefore, the 30°C incubation step was shortened to 5 hr using a Bio-Rad C1000 Touch thermal cycler (Bio-Rad, Hercules, CA, USA). DNA concentrations were measured in duplicate on a Qubit 2.0 with dsDNA High Sensitivity reagents (Invitrogen, Grand Island, NY, USA).</p>
<p><strong>Illumina library preparation and sequencing</strong></p>
<p>Two micrograms of MDA DNA were used to generate genome libraries using a TruSeq DNA PCR-Free Kit following the manufacturer’s protocol (Illumina, San Diego, CA, USA). The resulting libraries were sequenced using a Rapid-Run on an Illumina HiSeq 2500 (Center for Integrative Genomics, Georgia Institute of Technology) to obtain 100 bp paired-end reads</p>
Specified by the Principal Investigator(s)
<p><strong>BCO-DMO Processing</strong>:<br />
- Added cruise_id, lat and lon columns and created live links to NCBI pages.</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
PI Supplied Instrument Name: PI Supplied Instrument Description:Illumina HiSeq 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.
PI Supplied Instrument Name: PI Supplied Instrument Description:Bio-Rad C1000 Touch Thermocycler 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: JRES-204
JRES-204
R/V JOIDES Resolution
Community Standard Description
International Council for the Exploration of the Sea
R/V JOIDES Resolution
vessel
JRES-204
Gerhard Bohrmann
GEOMAR Kiel
http://dmoserv3.whoi.edu/data_docs/C-DEBI/cruise_reports/204PREL.PDF
Report describing JRES-204
R/V JOIDES Resolution
Community Standard Description
International Council for the Exploration of the Sea
R/V JOIDES Resolution
vessel