http://lod.bco-dmo.org/id/dataset/646128
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
2016-05-18
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Eukaryote transcriptome assemblies and associated metadata available on iMicrobe (P-ExpEv project)
2016-05-20
publication
2016-05-20
revision
BCO-DMO Linked Data URI
2016-05-20
creation
http://lod.bco-dmo.org/id/dataset/646128
Sonya T. Dyhrman
Lamont-Doherty Earth Observatory
principalInvestigator
Michael J. Follows
Massachusetts Institute of Technology
principalInvestigator
Richard E Lenski
Michigan State University
principalInvestigator
James Jeffrey Morris
University of Alabama at Birmingham
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. T., Lenski, R. E., Follows, M. J., Morris, J. J. (2016) Eukaryote transcriptome assemblies and associated metadata available on iMicrobe (P-ExpEv project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). Version Date 2016-05-20 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/646128 [access date]
Eukaryote transcriptome assemblies and associated metadata available on iMicrobe Dataset Description: <p>This dataset includes links to eukaryote transcriptome assemblies and associated metadata for species grown under replete nutrients and either modern or future CO2 concentrations. Further information on the overarching project and experiment details (e.g., nutrient concentrations, growth medium, GenBank BioSample IDs, etc) are available on iMicrobe MMETSP site: <a href="http://data.imicrobe.us/project/view/104" target="_blank">http://data.imicrobe.us/project/view/104</a> or by clicking on the accession numbers listed below.</p>
<p><strong>Accession &nbsp; &nbsp;&nbsp; Species/condition</strong><br />
<a href="http://data.imicrobe.us/sample/view/2475" target="_blank">MMETSP0053</a>&nbsp;Prorocentrum minimum&nbsp;(Pmi): replete;modern CO2<br />
<a href="http://data.imicrobe.us/sample/view/2477" target="_blank">MMETSP0057</a> Prorocentrum minimum (Pmi): replete; future CO2<br />
<a href="http://data.imicrobe.us/sample/view/2258" target="_blank">MMETSP0088</a> Chaetoceros affinis (Caf): replete;modern CO2<br />
<a href="http://data.imicrobe.us/sample/view/2261" target="_blank">MMETSP0092</a> Chaetoceros affinis (Caf): replete; future CO2<br />
<a href="http://data.imicrobe.us/sample/view/1716" target="_blank">MMETSP0093</a> Alexandrium monilatum (Amo): replete;modern CO2<br />
<a href="http://data.imicrobe.us/sample/view/1709" target="_blank">MMETSP0097</a> Alexandrium monilatum (Amo): replete; future CO2<br />
<a href="http://data.imicrobe.us/sample/view/1735" target="_blank">MMETSP0143</a> Chyrsochromulina polylepis (Cpo): replete;modern CO2<br />
<a href="http://data.imicrobe.us/sample/view/1746" target="_blank">MMETSP0147</a> Chrysochromulina polylepis (Cpo): replete; future CO2<br />
<a href="http://data.imicrobe.us/sample/view/1800" target="_blank">MMETSP0292</a> Heterosigma akashiwo (Hak): replete;modern CO2<br />
<a href="http://data.imicrobe.us/sample/view/1803" target="_blank">MMETSP0296</a> Heterosigma akashiwo (Hak): replete; future CO2<br />
<a href="http://data.imicrobe.us/sample/view/2199" target="_blank">MMETSP1363</a> Gephyrocapsa oceanica (Goc): replete;modern CO2<br />
<a href="http://data.imicrobe.us/sample/view/2200" target="_blank">MMETSP1364</a> Gephyrocapsa oceanica (Goc): replete; future CO2</p> Methods and Sampling: <p>The workflow for transcriptome assembly is described on the MMETSP website and is available at: <a href="http://marinemicroeukaryotes.org/home/faq" target="_blank">http://marinemicroeukaryotes.org/home/faq</a><strong>.&nbsp;</strong>Sequencing was done by the National Center for Genome Resources (NCGR).</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1314336 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1314336
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
Michael J. Follows
Massachusetts Institute of Technology
617-253-5939
54-1526, MIT 77 Massachusetts Avenue
Cambridge
MA
02139
USA
mick@mit.edu
pointOfContact
Richard E Lenski
Michigan State University
517-884-5397
567 Wilson Road #6177 Michigan State University
East Lansing
MI
48824
USA
lenski@msu.edu
pointOfContact
James Jeffrey Morris
University of Alabama at Birmingham
205-934-9498
1300 University Blvd CH253
Birmingham
AL
35294
USA
evolve@uab.edu
pointOfContact
asNeeded
Unknown
external_link
brief_desc
theme
None, User defined
external_link
brief description
featureType
BCO-DMO Standard Parameters
Automated DNA Sequencer
instrument
BCO-DMO Standard Instruments
Dyhrman_2013
service
Deployment Activity
Dyhrman lab, LDEO
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.
Science, Engineering and Education for Sustainability NSF-Wide Investment (SEES): Ocean Acidification (formerly CRI-OA)
https://www.nsf.gov/funding/pgm_summ.jsp?pims_id=503477
Science, Engineering and Education for Sustainability NSF-Wide Investment (SEES): Ocean Acidification (formerly CRI-OA)
NSF Climate Research Investment (CRI) activities that were initiated in 2010 are now included under Science, Engineering and Education for Sustainability NSF-Wide Investment (SEES). SEES is a portfolio of activities that highlights NSF's unique role in helping society address the challenge(s) of achieving sustainability. Detailed information about the SEES program is available from NSF (https://www.nsf.gov/funding/pgm_summ.jsp?pims_id=504707).
In recognition of the need for basic research concerning the nature, extent and impact of ocean acidification on oceanic environments in the past, present and future, the goal of the SEES: OA program is to understand (a) the chemistry and physical chemistry of ocean acidification; (b) how ocean acidification interacts with processes at the organismal level; and (c) how the earth system history informs our understanding of the effects of ocean acidification on the present day and future ocean.
Solicitations issued under this program:
NSF 10-530, FY 2010-FY2011
NSF 12-500, FY 2012
NSF 12-600, FY 2013
NSF 13-586, FY 2014
NSF 13-586 was the final solicitation that will be released for this program.
PI Meetings:
1st U.S. Ocean Acidification PI Meeting(March 22-24, 2011, Woods Hole, MA)
2nd U.S. Ocean Acidification PI Meeting(Sept. 18-20, 2013, Washington, DC)
3rd U.S. Ocean Acidification PI Meeting (June 9-11, 2015, Woods Hole, MA – Tentative)
NSF media releases for the Ocean Acidification Program:
Press Release 10-186 NSF Awards Grants to Study Effects of Ocean Acidification
Discovery Blue Mussels "Hang On" Along Rocky Shores: For How Long?
Discovery nsf.gov - National Science Foundation (NSF) Discoveries - Trouble in Paradise: Ocean Acidification This Way Comes - US National Science Foundation (NSF)
Press Release 12-179 nsf.gov - National Science Foundation (NSF) News - Ocean Acidification: Finding New Answers Through National Science Foundation Research Grants - US National Science Foundation (NSF)
Press Release 13-102 World Oceans Month Brings Mixed News for Oysters
Press Release 13-108 nsf.gov - National Science Foundation (NSF) News - Natural Underwater Springs Show How Coral Reefs Respond to Ocean Acidification - US National Science Foundation (NSF)
Press Release 13-148 Ocean acidification: Making new discoveries through National Science Foundation research grants
Press Release 13-148 - Video nsf.gov - News - Video - NSF Ocean Sciences Division Director David Conover answers questions about ocean acidification. - US National Science Foundation (NSF)
Press Release 14-010 nsf.gov - National Science Foundation (NSF) News - Palau's coral reefs surprisingly resistant to ocean acidification - US National Science Foundation (NSF)
Press Release 14-116 nsf.gov - National Science Foundation (NSF) News - Ocean Acidification: NSF awards $11.4 million in new grants to study effects on marine ecosystems - US National Science Foundation (NSF)
SEES-OA
largerWorkCitation
program
Impacts of Evolution on the Response of Phytoplankton Populations to Rising CO2
https://osprey.bco-dmo.org/project/2276
Impacts of Evolution on the Response of Phytoplankton Populations to Rising CO2
<p>Note: This project is also affiliated with the <a href="http://beacon-center.org/" target="_blank">NSF BEACON Center for the Study of Evolution in Action</a>.</p>
<p><em>Project Description from NSF Award:</em><br />
Human activities are driving up atmospheric carbon dioxide concentrations at an unprecedented rate, perturbing the ocean's carbonate buffering system, lowering oceanic pH, and changing the concentration and composition of dissolved inorganic carbon. Recent studies have shown that this ocean acidification has many short-term effects on phytoplankton, including changes in carbon fixation among others. These physiological changes could have profound effects on phytoplankton metabolism and community structure, with concomitant effects on Earth's carbon cycle and, hence, global climate. However, extrapolation of present understanding to the field are complicated by the possibility that natural populations might evolve in response to their changing environments, leading to different outcomes than those predicted from short-term studies. Indeed, evolution experiments demonstrate that microbes are often able to rapidly adapt to changes in the environment, and that beneficial mutations are capable of sweeping large populations on time scales relevant to predictions of environmental dynamics in the coming decades. This project addresses two major areas of uncertainty for phytoplankton populations with the following questions:<br />
1) What adaptive mutations to elevated CO2 are easily accessible to extant species, how often do they arise, and how large are their effects on fitness?<br />
2) How will physical and ecological interactions affect the expansion of those mutations into standing populations?</p>
<p>This study will address these questions by coupling experimental evolution with computational modeling of ocean biogeochemical cycles. First, cultured unicellular phytoplankton, representative of major functional groups (e.g. cyanobacteria, diatoms, coccolithophores), will be evolved under simulated year 2100 CO2 concentrations. From these experiments, estimates will be made of a) the rate of beneficial mutations, b) the magnitude of fitness gains conferred by these mutations, and c) secondary phenotypes (i.e., trade-offs) associated with these mutations, assayed using both physiological and genetic approaches. Second, an existing numerical model of the global ocean system will be modified to a) simulate the effects of changing atmospheric CO2 concentrations on ocean chemistry, and b) allow the introduction of CO2-specific adaptive mutants into the extant populations of virtual phytoplankton. The model will be used to explore the ecological and biogeochemical impacts of beneficial mutations in realistic environmental situations (e.g. resource availability, predation, etc.). Initially, the model will be applied to idealized sensitivity studies; then, as experimental results become available, the implications of the specific beneficial mutations observed in our experiments will be explored.</p>
<p>This interdisciplinary study will provide novel, transformative understanding of the extent to which evolutionary processes influence phytoplankton diversity, physiological ecology, and carbon cycling in the near-future ocean. One of many important outcomes will be the development and testing of nearly-neutral genetic markers useful for competition studies in major phytoplankton functional groups, which has applications well beyond the current proposal.</p>
P-ExpEv
largerWorkCitation
project
eng; USA
biota
oceans
Dyhrman lab, LDEO
-179.23
166.75
-64.7667
78.5922
2016-05-20
Experiment housed in laboratories at Michigan State University
0
BCO-DMO catalogue of parameters from Eukaryote transcriptome assemblies and associated metadata available on iMicrobe (P-ExpEv 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/646138.rdf
Name: external_link
Units: text
Description: <p>link to iMicrobe data repository</p>
http://lod.bco-dmo.org/id/dataset-parameter/646139.rdf
Name: brief_desc
Units: text
Description: <p>brief description of 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
1759
https://datadocs.bco-dmo.org/file/JEE1nGPIpMrmKA/MMETSP_data.csv
MMETSP_data.csv
Primary data file for dataset ID 646128
download
https://osprey.bco-dmo.org/dataset/646128/data/download
download
onLine
dataset
<p>The workflow for transcriptome assembly is described on the MMETSP website and is available at: <a href="http://marinemicroeukaryotes.org/home/faq" target="_blank">http://marinemicroeukaryotes.org/home/faq</a><strong>.&nbsp;</strong>Sequencing was done by the National Center for Genome Resources (NCGR).</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:Pacific Biosciences RS and Illumina HiSeq 2000 at NCGR 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.
Deployment: Dyhrman_2013
Dyhrman_2013
LDEO
laboratory
Dyhrman_2013
Sonya T. Dyhrman
Lamont-Doherty Earth Observatory
LDEO
laboratory