http://lod.bco-dmo.org/id/dataset/541197
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
2014-12-01
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Viral metagenome sequence data acquired in a study of the applicability of a new DNA sequencing technology for research problems in marine microbial ecology
2014-12-01
publication
2014-12-01
revision
BCO-DMO Linked Data URI
2014-12-01
creation
http://lod.bco-dmo.org/id/dataset/541197
Dr K Eric Wommack
University of Delaware
principalInvestigator
Dr Shawn W Polson
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: Wommack, K. E., Polson, S. W. (2014) Viral metagenome sequence data acquired in a study of the applicability of a new DNA sequencing technology for research problems in marine microbial ecology. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 01 Dec 2014) Version Date 2014-12-01 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/541197 [access date]
Viral metagenome sequence data Dataset Description: <p>This project focused on testing the applicability of a new DNA sequencing technology for research problems in marine microbial ecology. The data resulting from the project have been DNA sequence data that will ultimately be deposited in GenBank.</p>
<p><strong>Dataset Status (as of 01 December 2014): </strong>The investigators are currently analyzing the sequence data and expect that data will be deposited in GenBank by Q2 of 2015.</p> Methods and Sampling: <p>The genetic sequence data collected in this study will be deposited in GenBank.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1148118 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1148118
onGoing
Dr K Eric Wommack
University of Delaware
302-831-4362
Depts. Plant & Soil Sciences, Biological Sciences, and College of Earth, Ocean, & Environment Rm. 120C Delaware Biotechnology Institute, 15 Innovation Way
Newark
DE
19711
United States
wommack@dbi.udel.edu
pointOfContact
Dr Shawn W Polson
University of Delaware
302-831-3235
Dept. of Computer & Information Sciences and Dept. of Biological Sciences 15 Innovation Way, Rm 205F
Newark
DE
19711
United States
polson@dbi.udel.edu
pointOfContact
asNeeded
Dataset Version: 01 Dec 2014
Unknown
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.
Exploratory application of single-molecule real time (SMRT) DNA sequencing in microbial ecology research
http://virome.dbi.udel.edu
Exploratory application of single-molecule real time (SMRT) DNA sequencing in microbial ecology research
<p><em>Description from NSF award abstract:</em><br />
Microbial communities are the primary drivers of the global biogeochemical cycles that maintain the nutrient balance of ecosystems and ultimately shape overall ecosystem function. Today, we appreciate the critical role microbes play in the biochemical processing of nutrient elements; yet our understanding of how the structure of microbial communities influences the suite of biogeochemical processes within a given nutrient cycle is somewhat rudimentary. Limited understanding of structure-function relationships between microbial communities and biogeochemical cycles is due in large part to technological limitations in characterizing the ecology of microbial communities. Until recently, microbial ecologists simply had no means of unambiguously characterizing the richness and evenness of species within a microbial community and the prevailing biochemical capabilities of constituent microbial populations. Using high-throughput DNA sequencing and three methodological approaches, shotgun metagenomics, PCR amplicon sequencing, and genomics microbial ecologists are beginning to unveil the inner workings of microbial communities and connect genetic details with biogeochemical processes. While this work holds great promise for the advancement of microbial ecology, currently-available high-throughput sequencing technologies are not ideally suited to the high-sample throughput demands of ecosystem science, the small genome size of bacteria and viruses, and their genetic novelty. Moreover, in some cases the failure to adequately ground-truth application of next-generation DNA sequencers to environmental DNA samples has resulted in biased data and erroneous scientific conclusions.</p>
<p>This "high-risk; high-reward" research seeks to explore and test the use of a new, next-generation DNA sequencer, the PacBio RS, which has several attributes that may make it better suited to the specific needs of microbial ecology research and has the potential to be highly transformative to this geoscience discipline. A series of controlled and carefully replicated experiments will be conducted that will test the use of PacBio sequencing for shotgun metagenomics, 16S PCR amplicon sequencing, and single cell genome sequencing. This project will leverage existing datasets from other high-throughput sequencing platforms (e.g., Illumina and 454) to directly compare the performance of PacBio in each of these application areas. Through a NSF Major Research Instrumentation award to the University of Delaware, the PIs will have access to one of the few PacBio RS instruments available at an academic institution. Ultimately, these investigations will constrain the experimental error within PacBio sequencing and serve as an initial demonstration of the utility of the instrument for microbial ecology research.</p>
<p>Note: This is a collaborative research project, funded by NSF's EAGER mechanism.</p>
PacBio sequencing in microbial ecology
largerWorkCitation
project
eng; USA
biota
oceans
2014-12-01
Gulf of Maine and Chesapeake Bay
0
BCO-DMO catalogue of parameters from Viral metagenome sequence data acquired in a study of the applicability of a new DNA sequencing technology for research problems in marine microbial ecology
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
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
https://osprey.bco-dmo.org/dataset/541197/data/download
download
onLine
dataset
<p>The genetic sequence data collected in this study will be deposited in GenBank.</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