http://lod.bco-dmo.org/id/dataset/665853
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
2016-11-22
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
NCBI links to BioProjects of total RNA isolated from Trematomus bernacchii gill tissues acclimated to elevated temperature and pCO2, July 2015
2016-11-22
publication
2016-11-22
revision
BCO-DMO Linked Data URI
2016-11-22
creation
http://lod.bco-dmo.org/id/dataset/665853
Sean Place
Sonoma State University
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: Place, S. (2016) NCBI links to BioProjects of total RNA isolated from Trematomus bernacchii gill tissues acclimated to elevated temperature and pCO2, July 2015. Biological and Chemical Oceanography Data Management Office (BCO-DMO). Version Date 2016-11-22 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/665853 [access date]
NCBI RNA accessions for multi-stressor conditions of polar fishes Dataset Description: Methods and Sampling: <p>Specimens of <em>Trematomus&nbsp;</em><em>bernacchii</em><em>,&nbsp;Pagothenia&nbsp;</em><em>borchgrevinki</em><em>,</em>&nbsp;and <em>Trematomus&nbsp;</em><em>newnesi</em>&nbsp;were collected by hook and line near the Delbridge Islands in McMurdo Sound (77°40′S 166°25′E ) from October through&nbsp;December,&nbsp;2011 and September through&nbsp;December,&nbsp;2012. Once collected, fish were transported back to McMurdo Station in aerated coolers where they were acclimated for one week in a flow-through aquarium (2400-L) in ambient seawater (-1.5°C and ~430µatm CO2). After the initial acclimation period, fish were randomly placed into one of four flow-through experimental treatment tanks (1240-L each) in order to assess the response to increased temperature (4°C), increased pCO2 (1000µatm) or a combination of increased temperature and increased pCO2. The treatment tanks consisted of a tank held at ambient conditions (control treatment; -1°C and 430µatm), a low temperature + high pCO2 tank (-1°C and 1000µatm), a high temperature + low pCO2 tank (4°C and 430µatm), and a high temperature + high pCO2 tank (4°C and 1000µatm). <em>Trematomus&nbsp;</em><em>bernacchii</em><em>,&nbsp;Pagothenia&nbsp;</em><em>borchgrevinki</em>&nbsp;were sampled after t= 7, 28, and 56 days of acclimation to the experimental conditions. <em>Trematomus&nbsp;</em><em>newnesi</em>&nbsp;were sampled after t= 7, 28, and 42 days of acclimation. Four biological replicates from each treatment and time point were selected for cluster generation using the Illumina® TruSeq RNA Sample Prep v2 Hs Protocol and sequencing via an Illumina® HiSeq 2500 Rapid Run initialized for both paired-end 150bp reads and single-end 100bp reads.</p>
Funding provided by NSF Antarctic Sciences (NSF ANT) Award Number: PLR-1447291 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1447291
completed
Sean Place
Sonoma State University
(707)664-3054
Department of Biology 1801 East Cotati Avenue
Rohnert Park
CA
94928-3609
USA
places@sonoma.edu
pointOfContact
asNeeded
Unknown
project
location
lat
lon
species
NCBI_accession
accession_link
Illumina® HiSeq 2500
theme
None, User defined
project
site
latitude
longitude
species scientific name (binomial)
accession number
external_link
featureType
BCO-DMO Standard Parameters
Automated DNA Sequencer
instrument
BCO-DMO Standard Instruments
McMurdo_Place
service
Deployment Activity
McMurdo Station, Ross Sea
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
Identifying Adaptive Responses of Polar Fishes in a Vulnerable Ecosystem
https://osprey.bco-dmo.org/project/521649
Identifying Adaptive Responses of Polar Fishes in a Vulnerable Ecosystem
<p><em>Extracted from the NSF award abstract:</em></p>
<p>The proposed research will investigate the interacting and potentially synergistic influence of two oceanographic features - ocean acidification and the projected rise in mean sea surface temperature - on the performance of Notothenioids, the dominant fish of the Antarctic marine ecosystem. Understanding the joint effects of acidification and temperature rise on these fish is a vital component of predicting the resilience of coastal marine ecosystems. Notothenioids have repeatedly displayed a narrow window of physiological tolerances when subjected to abiotic stresses. Given that evolutionary adaptation may have led to finely-tuned traits with narrow physiological limits in these organisms, this system provides a unique opportunity to examine physiological trade-offs associated with acclimation to the multi-stressor environment expected from future atmospheric CO2 projections. Understanding these trade-offs will provide valuable insight into the capacity species have for responses to climate change via phenotypic plasticity. As an extension to functional measurements, this study will use evolutionary approaches to map variation in physiological responses onto the phylogeny of these fishes and the genetic diversity within species. These approaches offer insight into the historical constraints and future potential for evolutionary optimization.</p>
<p>Note: Funding for this project has transferred from award PLR-1040945 to PLR-1447291, coincident with Principal Investigator's affiliation change. Dr. Jeff Dudycha is a former project Co-PI associated with original award PLR-1040945.</p>
polar_fish_adapt
largerWorkCitation
project
eng; USA
biota
oceans
McMurdo Station, Ross Sea
2016-11-22
McMurdo Sound: Cape Evans, Cape Armitage, Delbridge Islands and Turks Head Bay
0
BCO-DMO catalogue of parameters from NCBI links to BioProjects of total RNA isolated from Trematomus bernacchii gill tissues acclimated to elevated temperature and pCO2, July 2015
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/665857.rdf
Name: project
Units: unitless
Description: <p>internal project identifier</p>
http://lod.bco-dmo.org/id/dataset-parameter/665858.rdf
Name: location
Units: unitless
Description: <p>specimen collection site</p>
http://lod.bco-dmo.org/id/dataset-parameter/665859.rdf
Name: lat
Units: decimal degrees
Description: <p>latitude; north is positive</p>
http://lod.bco-dmo.org/id/dataset-parameter/665860.rdf
Name: lon
Units: decimal degrees
Description: <p>longitude; east is positive</p>
http://lod.bco-dmo.org/id/dataset-parameter/665861.rdf
Name: species
Units: unitless
Description: <p>species name</p>
http://lod.bco-dmo.org/id/dataset-parameter/665862.rdf
Name: NCBI_accession
Units: unitless
Description: <p>NCBI Bioproject accession number</p>
http://lod.bco-dmo.org/id/dataset-parameter/665863.rdf
Name: accession_link
Units: unitless
Description: <p>link to NCBI BioProject page</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
605
https://datadocs.bco-dmo.org/file/WWW1r68hyYEN7g/RNA_seq.csv
RNA_seq.csv
Primary data file for dataset ID 665853
download
https://osprey.bco-dmo.org/dataset/665853/data/download
download
onLine
dataset
<p>Specimens of <em>Trematomus&nbsp;</em><em>bernacchii</em><em>,&nbsp;Pagothenia&nbsp;</em><em>borchgrevinki</em><em>,</em>&nbsp;and <em>Trematomus&nbsp;</em><em>newnesi</em>&nbsp;were collected by hook and line near the Delbridge Islands in McMurdo Sound (77°40′S 166°25′E ) from October through&nbsp;December,&nbsp;2011 and September through&nbsp;December,&nbsp;2012. Once collected, fish were transported back to McMurdo Station in aerated coolers where they were acclimated for one week in a flow-through aquarium (2400-L) in ambient seawater (-1.5°C and ~430µatm CO2). After the initial acclimation period, fish were randomly placed into one of four flow-through experimental treatment tanks (1240-L each) in order to assess the response to increased temperature (4°C), increased pCO2 (1000µatm) or a combination of increased temperature and increased pCO2. The treatment tanks consisted of a tank held at ambient conditions (control treatment; -1°C and 430µatm), a low temperature + high pCO2 tank (-1°C and 1000µatm), a high temperature + low pCO2 tank (4°C and 430µatm), and a high temperature + high pCO2 tank (4°C and 1000µatm). <em>Trematomus&nbsp;</em><em>bernacchii</em><em>,&nbsp;Pagothenia&nbsp;</em><em>borchgrevinki</em>&nbsp;were sampled after t= 7, 28, and 56 days of acclimation to the experimental conditions. <em>Trematomus&nbsp;</em><em>newnesi</em>&nbsp;were sampled after t= 7, 28, and 42 days of acclimation. Four biological replicates from each treatment and time point were selected for cluster generation using the Illumina® TruSeq RNA Sample Prep v2 Hs Protocol and sequencing via an Illumina® HiSeq 2500 Rapid Run initialized for both paired-end 150bp reads and single-end 100bp reads.</p>
Specified by the Principal Investigator(s)
<p><strong>BCO-DMO Processing Notes:&nbsp;</strong>A flat file table of the accession numbers with associated metadata and links to NCBI was created and served.</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
Illumina® HiSeq 2500
Illumina® HiSeq 2500
PI Supplied Instrument Name: Illumina® HiSeq 2500 PI Supplied Instrument Description:For genetic sequencing 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: McMurdo_Place
McMurdo_Place
McMurdo Station
laboratory
McMurdo_Place
Sean Place
Sonoma State University
McMurdo Station
laboratory