http://lod.bco-dmo.org/id/dataset/546404
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
2015-01-30
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Experimental results: microarrays for Thalassiosira pseudonana diatoms grown in the laboratory under different conditions; 2013 (OA Diatom Response project)
2015-01-30
publication
2015-01-30
revision
BCO-DMO Linked Data URI
2015-01-30
creation
http://lod.bco-dmo.org/id/dataset/546404
Monica V. Orellana
Institute for Systems Biology
principalInvestigator
Nitin Baliga
Institute for Systems Biology
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: Orellana, M. V., Baliga, N. (2015) Experimental results: microarrays for Thalassiosira pseudonana diatoms grown in the laboratory under different conditions; 2013 (OA Diatom Response project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 30 Jan 2015) Version Date 2015-01-30 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/546404 [access date]
Microarrays for T. pseudonana diatoms grown in the laboratory under different conditions. Dataset Description: <p>Microarrays for <em>Thalassiosira pseudonana</em> diatoms grown in the laboratory under different conditions including<br />
diel cycles and elevated CO2 levels.</p>
<p>Data from Ashworth et al. (2013) Proc. Natl. Acad. Sci. USA 110(18):7518-23 are publicly available on the NCBI GEO database under the accession code: <a href="http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE45252" target="_blank">GSE45252</a>.</p>
<p>Data were submitted to the NCBI GEO database on May 16, 2014 under the accession code: <a href="http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE57737" target="_blank">GSE57737</a> and will be made publicly available upon publication of an accompanying manuscript in preparation.</p>
<p><strong>References:</strong><br />
Ashworth J, Coesel S, Lee A, Armbrust EV, Orellana MO*, Baliga NS*. (2013) Genome-wide diel growth state transitions in the diatom Thalassiosira pseudonana. Proc. Natl. Acad. Sci. 110(18):7518-23. doi:<a href="http://dx.doi.org/10.1073/pnas.1300962110" target="_blank">10.1073/pnas.1300962110</a></p> Methods and Sampling: <p>Transcriptomic profiling of the diatom <em>Thalassiosira pseudonana</em> at normal and elevlated CO2 levels and at normal and elevated light levels. Common reference total RNA (Agilent Quick-Amp Cy3-labeled) was used in all arrays as an internal standard. Triplicate batch cultures grown at normal (~400 ppm) and elevated (~800 ppm) CO2 levels, both at i) normal or ii) elevated light levels. Samples were taken during a) exponential and b) stationary growth during all growth experiments.</p>
<p>Result: 48 total transcriptomic measurements: [3 parallel replicates] x [400 ppm, 800 ppm] x [normal light, high<br />
light] x [exponential, stationary] x [2 serial replicates].</p>
Funding provided by NSF Emerging Frontiers Division (NSF EF) Award Number: EF-1316206 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1316206
onGoing
Monica V. Orellana
Institute for Systems Biology
Institute for Systems Biology 401 Terry Avenue North
Seattle
WA
98109
USA
monica.orellana@isbscience.org
pointOfContact
Nitin Baliga
Institute for Systems Biology
401 Terry Ave N
Seattle
WA
98109
USA
nitin.baliga@systemsbiology.org
pointOfContact
asNeeded
Dataset Version: 30 Jan 2015
Unknown
taxon
publication
GEO_accession
theme
None, User defined
taxon
reference_paper
accession number
featureType
BCO-DMO Standard Parameters
ISB_Orellana
service
Deployment Activity
Seattle, WA
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
A Systems Biology Approach to Characterize Diatom Response to Ocean Acidification and Climate Change
https://osprey.bco-dmo.org/project/546207
A Systems Biology Approach to Characterize Diatom Response to Ocean Acidification and Climate Change
<p><em>Description from the NSF award abstract:</em><br />
Diatoms account for approximately 40 percent of primary production in the world's oceans and are the most productive marine phytoplankton group. They form the basis of food webs in coastal and ocean upwelling areas that support important fisheries and have a major role in global carbon and silicon cycles. The goal of this project is to understand the impact of ocean acidification, in combination with other stressors, on the marine diatom <em>Thalassiosira pseudonana</em>. This project will generate a predictive model of expression of all genes of this diatom that can be used to forecast the diatom's response to projected environmental scenarios to an acidifying ocean. A combination of laboratory and field studies will be used; diatoms will be grown under carbon dioxide concentrations that reflect today's values as well as future predicted conditions and light levels and nutrients concentrations will also be varied. Physiological and gene expression responses will be measured and integrated using computational and modeling methods to gain an unbiased, systems-level understanding of the response of diatoms to ocean acidification. This combined approach will enable the forecasting and prediction of the diatom's response to environmental change and the elucidation and genomic interpretation of biochemically relevant processes in natural environment.</p>
OA Diatom Response
largerWorkCitation
project
eng; USA
biota
oceans
Seattle, WA
2015-01-30
0
BCO-DMO catalogue of parameters from Experimental results: microarrays for Thalassiosira pseudonana diatoms grown in the laboratory under different conditions; 2013 (OA Diatom Response 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/546467.rdf
Name: taxon
Units: text
Description: <p>Taxon/species of study.</p>
http://lod.bco-dmo.org/id/dataset-parameter/546468.rdf
Name: publication
Units: text
Description: <p>Publication where the details of the study can be found.</p>
<p>Ashworth_et_al_2013 = Ashworth J, Coesel S, Lee A, Armbrust EV, Orellana MO*, Baliga NS*. (2013) Genome-wide diel growth state transitions in the diatom Thalassiosira pseudonana. Proc. Natl. Acad. Sci. 110(18):7518-23. doi:<a href="http://dx.doi.org/10.1073/pnas.1300962110" target="_blank">10.1073/pnas.1300962110</a></p>
http://lod.bco-dmo.org/id/dataset-parameter/546469.rdf
Name: GEO_accession
Units: alphanumeric
Description: <p>Accession number and hyperlink to the NCBI GEO database.</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
406
https://datadocs.bco-dmo.org/file/QAAXxYRtBQW986/Thaps_microarrays.csv
Thaps_microarrays.csv
Primary data file for dataset ID 546404
download
https://osprey.bco-dmo.org/dataset/546404/data/download
download
onLine
dataset
<p>Transcriptomic profiling of the diatom <em>Thalassiosira pseudonana</em> at normal and elevlated CO2 levels and at normal and elevated light levels. Common reference total RNA (Agilent Quick-Amp Cy3-labeled) was used in all arrays as an internal standard. Triplicate batch cultures grown at normal (~400 ppm) and elevated (~800 ppm) CO2 levels, both at i) normal or ii) elevated light levels. Samples were taken during a) exponential and b) stationary growth during all growth experiments.</p>
<p>Result: 48 total transcriptomic measurements: [3 parallel replicates] x [400 ppm, 800 ppm] x [normal light, high<br />
light] x [exponential, stationary] x [2 serial replicates].</p>
Specified by the Principal Investigator(s)
<p>Array slides were scanned using an Agilent slide scanner. Data were processed from Agilent files using the limma package in R, including background correction, loess (within-array) and 'Aquantile' (between-array) normalization.</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
Deployment: ISB_Orellana
ISB_Orellana
Institute for Systems Biology
laboratory
ISB_Orellana
Monica V. Orellana
Institute for Systems Biology
Institute for Systems Biology
laboratory