http://lod.bco-dmo.org/id/dataset/626263
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
2015-11-10
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Accession numbers for raw sequence reads; samples collected on R/V Roger Revelle cruise KNOX02RR in the South Pacific Gyre from 2006-2007 (Microbial Diversity SPG project)
2015-11-10
publication
2015-11-10
revision
BCO-DMO Linked Data URI
2015-11-10
creation
http://lod.bco-dmo.org/id/dataset/626263
Dr John Heidelberg
University of Southern California
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: Heidelberg, J. (2015) Accession numbers for raw sequence reads; samples collected on R/V Roger Revelle cruise KNOX02RR in the South Pacific Gyre from 2006-2007 (Microbial Diversity SPG project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 10 November 2015) Version Date 2015-11-10 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/626263 [access date]
Accession numbers for raw sequence reads; samples collected on cruise KNOX02RR. Dataset Description: <p>Accession numbers from the NCBI SRA for 16S amplicons; samples collected on KNOX02RR.</p> Methods and Sampling: <p>All methodology can be located in the reference:<br />
Tully and Heidelberg 2013. Microbial communities associated with ferromanganese nodules and the surrounding sediments. Frontiers in Microbiology. 4(161). doi:<a href="http://dx.doi.org/10.3389/fmicb.2013.00161" target="_blank">10.3389/fmicb.2013.00161</a></p>
<p>In summary (refer to publication above for complete description of methodology):<br />
Sediment and FeMn nodules were collected during Expedition Knox-02RR (December 2006–January 2007 aboard the R/V <em>Roger Revelle</em>). Extraction of DNA from nodules proceeded using a modified phenol-chloroform extraction method. Due to low yield using the described phenol-chloroform method, extraction of DNA from sediment samples was performed using the MoBio PowerLyzer PowerSoil DNA kit following the manufacturer's protocol. All samples with &gt;0.1 ng/uL final DNA concentration were cleaned and concentrated and samples were resuspended in 20 uL of sterile, DNase-free H2O. Samples were amplified using PCR, targeting the V4 region of the 16S rRNA gene. All amplifications were performed using the FastStart High Fidelity PCR System (Roche). Initial PCR products were pooled and the PCR product (~550 bp) was gel excised using the Qiagen Gel Extraction Kit (Qiagen) following the manufacturer's protocol. Excised DNA products were amplified in duplicate to generate sufficient material for pyrosequencing. PCR products were pooled and cleaned using the AMPure Bead XP (Agencourt) kit, following the manufacturer's protocol. Samples were quantified using PicoGreen and visualized using Agilent Bioanalyzer using the High Sensitivity (Agilent) chip.</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
Dr John Heidelberg
University of Southern California
213-740-5791
AHF 107 University Park
Los Angeles
CA
90089-0701
jheidelb@usc.edu
pointOfContact
asNeeded
Dataset Version: 10 November 2015
Unknown
cruise_id
bioproject_ID
SRA_ID
strategy
source
selection
primer
bioproject_URL
SRA_URL
accession_ID
accession_URL
sample_name
sample_name2
sample_description
sample_location
lat
lon
sample_depth
method
barcode
Qubit 1.0
PCR
theme
None, User defined
Cruise identfier
No BCO-DMO term
latitude
longitude
featureType
BCO-DMO Standard Parameters
Fluorometer
Thermal Cycler
instrument
BCO-DMO Standard Instruments
KNOX02RR
service
Deployment Activity
South Pacific Gyre
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
Deep phylogenetic and metagenomic analysis of microbial diversity associated with ferromanganese nodules collected from the South Pacific Gyre
https://osprey.bco-dmo.org/project/626257
Deep phylogenetic and metagenomic analysis of microbial diversity associated with ferromanganese nodules collected from the South Pacific Gyre
<p><em>Project description obtained from <a href="http://www.darkenergybiosphere.org/education/graduatesFunded.html" target="_blank">C-DEBI</a>:</em><br />
The importance of microbial mediation in the biogeochemical cycles of the ocean is well documented. A major source of marine metallic minerals exists as ferromanganese (polymetallic) nodules in the deep ocean (4,000-5,000 m deep). Composed predominantly of iron, manganese, copper, nickel, and zinc, these nodules play a key role in governing the biogeochemical availability of many of these metals in the global ocean. While it is assumed that microorganisms mediate some of the processes that form nodules, it is poorly constrained as to which organisms mediate these processes or how these processes in turn may support microbial metabolisms. We propose using fingerprinting and sequencing methods to examine the microbial community diversity of organism associated with ferromanganese nodule collected from the South Pacific Gyre. Further, because many of the microbial organisms present in the deep-sea are novel and uncultivated, we plan to perform metagenomic analysis to link phylogenetic identity with physiology, with the goal of generating (near-)complete environmental genomes. The proposed research will be the first attempt to determine how the microbiology of deep oceanic nodules shape and are shaped by the environment.</p>
<p>This project was funded by a C-DEBI Graduate Student Fellowship.</p>
Microbial Diversity SPG
largerWorkCitation
project
eng; USA
biota
oceans
South Pacific Gyre
2015-11-10
Central South Pacific Gyre (39.3103S, 139.8006 W)
0
BCO-DMO catalogue of parameters from Accession numbers for raw sequence reads; samples collected on R/V Roger Revelle cruise KNOX02RR in the South Pacific Gyre from 2006-2007 (Microbial Diversity SPG 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/626278.rdf
Name: cruise_id
Units: dimensionless
Description: <p>Cruise identification number.</p>
http://lod.bco-dmo.org/id/dataset-parameter/626279.rdf
Name: bioproject_ID
Units: dimensionless
Description: <p>NCBI BioProject ID number.</p>
http://lod.bco-dmo.org/id/dataset-parameter/626280.rdf
Name: SRA_ID
Units: dimensionless
Description: <p>NCBI SRA ID number.</p>
http://lod.bco-dmo.org/id/dataset-parameter/626281.rdf
Name: strategy
Units: dimensionless
Description: <p>16S rRNA hypervariable gene amplification.</p>
http://lod.bco-dmo.org/id/dataset-parameter/626282.rdf
Name: source
Units: dimensionless
Description: <p>Various samples collected via multicore instrument.</p>
http://lod.bco-dmo.org/id/dataset-parameter/626283.rdf
Name: selection
Units: dimensionless
Description: <p>Available aseptic samples.</p>
http://lod.bco-dmo.org/id/dataset-parameter/626284.rdf
Name: primer
Units: dimensionless
Description: <p>Primer used. FU515-GTGY CAGCMGCCGCGGTA & RU1048-CGRCRCCATGYANCWC</p>
http://lod.bco-dmo.org/id/dataset-parameter/626285.rdf
Name: bioproject_URL
Units: dimensionless
Description: <p>Hyperlink to NCBI BioProject.</p>
http://lod.bco-dmo.org/id/dataset-parameter/626286.rdf
Name: SRA_URL
Units: dimensionless
Description: <p>Hyperlink to NCBI SRA.</p>
http://lod.bco-dmo.org/id/dataset-parameter/626287.rdf
Name: accession_ID
Units: dimensionless
Description: <p>NCBI accession number.</p>
http://lod.bco-dmo.org/id/dataset-parameter/626288.rdf
Name: accession_URL
Units: dimensionless
Description: <p>Hyperlink to NCBI accession.</p>
http://lod.bco-dmo.org/id/dataset-parameter/626289.rdf
Name: sample_name
Units: dimensionless
Description: <p>Sample identifer.</p>
http://lod.bco-dmo.org/id/dataset-parameter/626290.rdf
Name: sample_name2
Units: dimensionless
Description: <p>Sample identifer.</p>
http://lod.bco-dmo.org/id/dataset-parameter/626291.rdf
Name: sample_description
Units: dimensionless
Description: <p>Description of the sample: Surface sediments and ferromanganese nodules.</p>
http://lod.bco-dmo.org/id/dataset-parameter/626292.rdf
Name: sample_location
Units: dimensionless
Description: <p>Location of sampling: South Pacific Ocean, central gyre.</p>
http://lod.bco-dmo.org/id/dataset-parameter/626293.rdf
Name: lat
Units: decimal degrees
Description: <p>Latitude of sample collection.</p>
http://lod.bco-dmo.org/id/dataset-parameter/626294.rdf
Name: lon
Units: decimal degrees
Description: <p>Longitude of sample collection.</p>
http://lod.bco-dmo.org/id/dataset-parameter/626295.rdf
Name: sample_depth
Units: meters
Description: <p>Depth at which sample was collected.</p>
http://lod.bco-dmo.org/id/dataset-parameter/626296.rdf
Name: method
Units: dimensionless
Description: <p>DNA extraction method; via phenol:chloroform method</p>
http://lod.bco-dmo.org/id/dataset-parameter/626297.rdf
Name: barcode
Units: dimensionless
Description: <p>DNA barcode.</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
14832
https://datadocs.bco-dmo.org/file/XYYPG3VU4v4Ron/SPG_accession_nums.csv
SPG_accession_nums.csv
Primary data file for dataset ID 626263
download
https://osprey.bco-dmo.org/dataset/626263/data/download
download
onLine
dataset
<p>All methodology can be located in the reference:<br />
Tully and Heidelberg 2013. Microbial communities associated with ferromanganese nodules and the surrounding sediments. Frontiers in Microbiology. 4(161). doi:<a href="http://dx.doi.org/10.3389/fmicb.2013.00161" target="_blank">10.3389/fmicb.2013.00161</a></p>
<p>In summary (refer to publication above for complete description of methodology):<br />
Sediment and FeMn nodules were collected during Expedition Knox-02RR (December 2006–January 2007 aboard the R/V <em>Roger Revelle</em>). Extraction of DNA from nodules proceeded using a modified phenol-chloroform extraction method. Due to low yield using the described phenol-chloroform method, extraction of DNA from sediment samples was performed using the MoBio PowerLyzer PowerSoil DNA kit following the manufacturer's protocol. All samples with &gt;0.1 ng/uL final DNA concentration were cleaned and concentrated and samples were resuspended in 20 uL of sterile, DNase-free H2O. Samples were amplified using PCR, targeting the V4 region of the 16S rRNA gene. All amplifications were performed using the FastStart High Fidelity PCR System (Roche). Initial PCR products were pooled and the PCR product (~550 bp) was gel excised using the Qiagen Gel Extraction Kit (Qiagen) following the manufacturer's protocol. Excised DNA products were amplified in duplicate to generate sufficient material for pyrosequencing. PCR products were pooled and cleaned using the AMPure Bead XP (Agencourt) kit, following the manufacturer's protocol. Samples were quantified using PicoGreen and visualized using Agilent Bioanalyzer using the High Sensitivity (Agilent) chip.</p>
Specified by the Principal Investigator(s)
<p>Data processing can be located in the reference:<br />
Tully and Heidelberg 2013. Microbial communities associated with ferromanganese nodules and the surrounding sediments. Frontiers in Microbiology. 4(161). doi:<a href="http://dx.doi.org/10.3389/fmicb.2013.00161" target="_blank">10.3389/fmicb.2013.00161</a></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
Qubit 1.0
Qubit 1.0
PI Supplied Instrument Name: Qubit 1.0 PI Supplied Instrument Description:Samples were then quantified using the Qubit 1.0 fluorometer and the Qubit dsDNA HS Assay Kit (Life Technologies). Instrument Name: Fluorometer Instrument Short Name:Fluorometer Instrument Description: A fluorometer or fluorimeter is a device used to measure parameters of fluorescence: its intensity and wavelength distribution of emission spectrum after excitation by a certain spectrum of light. The instrument is designed to measure the amount of stimulated electromagnetic radiation produced by pulses of electromagnetic radiation emitted into a water sample or in situ. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/113/
PCR
PCR
PI Supplied Instrument Name: PCR PI Supplied Instrument Description:Samples were amplified using PCR, targeting the V4 region of the 16S rRNA gene. All amplifications were performed using the FastStart High Fidelity PCR System (Roche). 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: KNOX02RR
KNOX02RR
R/V Roger Revelle
Community Standard Description
International Council for the Exploration of the Sea
R/V Roger Revelle
vessel
KNOX02RR
Steven L. D'Hondt
University of Rhode Island
R/V Roger Revelle
Community Standard Description
International Council for the Exploration of the Sea
R/V Roger Revelle
vessel