http://lod.bco-dmo.org/id/dataset/628253
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
2015-12-04
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Metagenomes from Delaware estuarine riverbank sediments obtained by push corer in July 2012
2015-12-04
publication
2015-12-04
revision
BCO-DMO Linked Data URI
2015-12-04
creation
http://lod.bco-dmo.org/id/dataset/628253
Jennifer F. Biddle
University of Delaware
principalInvestigator
Dr Adam Marsh
University of Delaware
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: Biddle, J. F., Marsh, A. (2015) Metagenomes from Delaware estuarine riverbank sediments obtained by push corer in July 2012. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 04 Dec 2015) Version Date 2015-12-04 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/628253 [access date]
Metagenomes from Delaware estuarine riverbank sediment. Dataset Description: <p>Metagenomes from Delaware estuarine riverbank sediment.</p> Methods and Sampling: <p><strong>Sample collection and storage:</strong> A riverbank sediment core was extracted from the Oyster Rocks site of the Broadkill River in Milton, Delaware in July 2012, accessed on foot. Extraction was performed with a polycarbonate push core. Samples were taken in 3 cm slices along the depth of the core and frozen at -80 degrees C until DNA extractions were performed.</p>
<p><strong>DNA digestion and Illumina sequencing:</strong> DNA was extracted using a MoBio Powersoil DNA kit. Extracted DNA was digested with HpaII restriction endonuclease. Illumina library preparation and 150-cycle single-read sequencing was performed on an Illumina Hi-Seq 2500 at the University of Delaware Sequencing and Genotyping Center (Delaware Biotechnology Institute).</p>
<p>Raw reads are publicly available through the European Nucleotide Archive at <a href="http://www.ebi.ac.uk/ena/data/view/ERP013107" target="_blank">http://www.ebi.ac.uk/ena/data/view/ERP013107</a></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 F. Biddle
University of Delaware
302-645-4267
College of Earth, Ocean, and Environment 212 Cannon Laboratory
Lewes
Delaware
19958
USA
jfbiddle@udel.edu
pointOfContact
Dr Adam Marsh
University of Delaware
302-645-4367
700 Pilottown Rd.
Lewes
Delaware
19958
United States
amarsh@udel.edu
pointOfContact
asNeeded
Dataset Version: 04 Dec 2015
Unknown
site
lat
lon
description
ENA_ID
ENA_URL
polycarbonate push core
theme
None, User defined
site
latitude
longitude
brief description
accession number
No BCO-DMO term
featureType
BCO-DMO Standard Parameters
Push Corer
instrument
BCO-DMO Standard Instruments
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
Metagenomic analysis of microbial CpG methylation in Delaware estuarine riverbank sediment
https://osprey.bco-dmo.org/project/628237
Metagenomic analysis of microbial CpG methylation in Delaware estuarine riverbank sediment
<p>Marine sediments harbor a vast amount of Earth’s microbial biomass, yet little is understood regarding how cells subsist in these low-energy environments without forming endospores. DNA methylation, a reversible process that involves the addition of a methyl group to a nucleotide base via a methyltransferase, exists as a possible epigenetic mechanism for non-sporulated cells in low-energy sediment environments to regulate gene expression and potentially lower cellular activity. To investigate the presence and scope of this phenomenon in estuarine sediment microbial communities, we sequenced three metagenomic and 16S rRNA gene amplicon libraries extracted from a sediment core collected from the banks of the Oyster Rocks site of the Broadkill River, Milton, Delaware, USA. We targeted 5-methylcytosine at CpG sites by digesting metagenomic libraries with the methylation-sensitive restriction endonuclease HpaII. By quantitatively distinguishing "mixed" methylation states for populations of CpG site copies, we identified dynamic, non-binary shifts in CpG methylation for community taxa and function.</p>
Microbial CpG Methylation
largerWorkCitation
project
eng; USA
biota
oceans
2015-12-04
Delaware River estuary
0
BCO-DMO catalogue of parameters from Metagenomes from Delaware estuarine riverbank sediments obtained by push corer in July 2012
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/628267.rdf
Name: site
Units: dimensionless
Description: <p>Description/name of site.</p>
http://lod.bco-dmo.org/id/dataset-parameter/628268.rdf
Name: lat
Units: decimal degrees
Description: <p>Latitude of sampling site.</p>
http://lod.bco-dmo.org/id/dataset-parameter/628269.rdf
Name: lon
Units: decimal degrees
Description: <p>Longitude of sampling site. (Negative = West)</p>
http://lod.bco-dmo.org/id/dataset-parameter/628270.rdf
Name: description
Units: dimensionless
Description: <p>Brief description of the data.</p>
http://lod.bco-dmo.org/id/dataset-parameter/628271.rdf
Name: ENA_ID
Units: dimensionless
Description: <p>Project ID number in the European Nucleotide Archive.</p>
http://lod.bco-dmo.org/id/dataset-parameter/628272.rdf
Name: ENA_URL
Units: dimensionless
Description: <p>Hyperlink to European Nucleotide Archive for this project ID.</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
212
https://datadocs.bco-dmo.org/file/B11vMzjtP7D4rM/OysterRocks_metagenomes.csv
OysterRocks_metagenomes.csv
Primary data file for dataset ID 628253
download
https://osprey.bco-dmo.org/dataset/628253/data/download
download
onLine
dataset
<p><strong>Sample collection and storage:</strong> A riverbank sediment core was extracted from the Oyster Rocks site of the Broadkill River in Milton, Delaware in July 2012, accessed on foot. Extraction was performed with a polycarbonate push core. Samples were taken in 3 cm slices along the depth of the core and frozen at -80 degrees C until DNA extractions were performed.</p>
<p><strong>DNA digestion and Illumina sequencing:</strong> DNA was extracted using a MoBio Powersoil DNA kit. Extracted DNA was digested with HpaII restriction endonuclease. Illumina library preparation and 150-cycle single-read sequencing was performed on an Illumina Hi-Seq 2500 at the University of Delaware Sequencing and Genotyping Center (Delaware Biotechnology Institute).</p>
<p>Raw reads are publicly available through the European Nucleotide Archive at <a href="http://www.ebi.ac.uk/ena/data/view/ERP013107" target="_blank">http://www.ebi.ac.uk/ena/data/view/ERP013107</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
polycarbonate push core
polycarbonate push core
PI Supplied Instrument Name: polycarbonate push core PI Supplied Instrument Description:A riverbank sediment core was extracted from the Oyster Rocks site of the Broadkill River in Milton, Delaware in July 2012. Extraction was performed with a polycarbonate push core. Instrument Name: Push Corer Instrument Short Name: Instrument Description: Capable of being performed in numerous environments, push coring is just as it sounds. Push coring is simply pushing the core barrel (often an aluminum or polycarbonate tube) into the sediment by hand. A push core is useful in that it causes very little disturbance to the more delicate upper layers of a sub-aqueous sediment.
Description obtained from: http://web.whoi.edu/coastal-group/about/how-we-work/field-methods/coring/