http://lod.bco-dmo.org/id/dataset/627996
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
2015-12-02
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
cDNA expressed sequence tags for the corals Acropora palmate and Orbicella faveola in Mexico, Panama, and the Florida Keys in 2003 (SymBioSys project)
2016-02-01
publication
2016-02-01
revision
BCO-DMO Linked Data URI
2016-02-01
creation
http://lod.bco-dmo.org/id/dataset/627996
Mónica Medina
University of California-Merced
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: Medina, M. (2016) cDNA expressed sequence tags for the corals Acropora palmate and Orbicella faveola in Mexico, Panama, and the Florida Keys in 2003 (SymBioSys project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 2016-02-01) Version Date 2016-02-01 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/627996 [access date]
cDNA Expressed Sequence Tags for the corals Acropora palmate and Orbicella faveola Dataset Description: <p>This dataset includes links to NCBI accession pages for cDNA EST's for the corals <em>Acropora palmate</em> and <em>Orbicella faveola</em> (<em>Montastraea faveolata</em>).</p>
<p><strong>Related References:</strong></p>
<p>Desalvo, MK., CR. Voolstra, S. Sunagawa, JA. Schwarz, JH. Stillman, MA. Coffroth, AM. Szmant and M. Medina (2008) Differential gene expression during thermal stress and bleaching in the Caribbean coral <em>Montastraea faveolata. </em>Molecular Ecology, doi: 10.1111/j.1365-294X.2008.03879.x</p>
<p>Desalvo, MK., S. Sunagawa, PL. Fisher, CR. Voolstra, R. Iglesias-Prieto and M. Medina (2010) Coral host transcriptomic states are correlated with Symbiodinium genotypes. Molecular Ecology, 19, 1174–1186 doi: 10.1111/j.1365-294X.2010.04534.x</p>
<p>DeSalvo MK., S Sunagawa, CR. Voolstra, M. Medina (2010) Transcriptomic responses to heat stress and bleaching in the elkhorn coral <em>Acropora palmate. </em>Mar Ecol Prog Ser, 402: 97–113, doi: 10.3354/meps08372</p>
<p>DeSalvo MK., A. Estrada, S. Sunagawa, M. Medina (2011) Transcriptomic responses to darkness stress point to common coral bleaching mechanisms. Coral Reefs, doi 10.1007/s00338-011-0833-4.</p>
<p>Schwarz JA, PB Brokstein, C Voolstra, AY Terry, DJ Miller, AM Szmant, MA Coffroth and M Medina (2008) Coral life history and symbiosis: Functional genomic resources for two reef building Caribbean corals, <em>Acropora palmata </em>and <em>Montastraea faveolata</em>. BMC Genomics, 9:97, doi:10.1186/1471-2164-9-97.</p>
<p>Voolstra CR., JA. Schwarz, J Schnetzer,S Sunagawa,MK. Desalvo, AM. Szmant, MA Coffroth and M Medina (2009) The host transcriptome remains unaltered during the establishment of coral–algal symbioses.&nbsp;Molecular Ecology, 18, 1823–1833, doi: 10.1111/j.1365-294X.2009.04167.x</p> Methods and Sampling: <p>Coral spawn and adult fragments were collected in the Florida Keys in a shallow reef environment at 30 ft. by scuba. RNA was extracted following standard protocols from Ambion kits. Samples were QCed with Nanodrop and Bionalyzer instruments and cDNA libraries were built for EST sequencing.</p>
<p><strong>Protocols:</strong><br />
<a href="http://dmoserv3.bco-dmo.org/data_docs/SymBioSys/Coral-RNA-isolation-protocol-for-small-preps-in-1.5mL-or-2mL-tubes.pdf" target="_blank">Coral RNA isolation protocol (for small prep’s in 1.5mL or 2mL tubes)</a><br />
<a href="http://dmoserv3.bco-dmo.org/data_docs/SymBioSys/Coral-RNA-isolation-for-large-preps-in-15mL-Falcon-tubes.pdf" target="_blank">Coral RNA isolation (for large prep’s in 15mL Falcon tubes)</a></p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-0926906 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=0926906
completed
Mónica Medina
University of California-Merced
814-321-5684
326 Mueller
University Park
PA
16802
USA
momedinamunoz@gmail.com
pointOfContact
asNeeded
Dataset Version: 2016-02-01
Unknown
species
experiment
molecule_type
lat_PMor_Mex
lon_PMor_Mex
lat_KLar_FL
lon_KLar_FL
lat_CZap_Pan
lon_CZap_Pan
lat_ISol_Pan
lon_ISol_Pan
lat_CraK_Pan
lon_CraK_Pan
comment
GenBank_GI
GenBank_ACC
EST_Name
direction_seq
theme
None, User defined
species scientific name (binomial)
brief description
No BCO-DMO term
latitude
longitude
comments
accession number
featureType
BCO-DMO Standard Parameters
Automated DNA Sequencer
Thermal Cycler
instrument
BCO-DMO Standard Instruments
Medina_genomics
service
Deployment Activity
coral reefs in Mexico, Panama, Florida Keys
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.
Ontogenic change in Cnidarian-algal symbioses: A genomic and ecologic perspective
https://osprey.bco-dmo.org/project/472478
Ontogenic change in Cnidarian-algal symbioses: A genomic and ecologic perspective
<p>PROJECT SUMMARY:<br />
The symbiosis between corals (Cnidaria:Hexacorallia:Scleractinia) and photosynthetic dinoflagellate symbionts (Alveolata: Dinophycea: Symbiodinium) provides the foundation and structure of the coral reef ecosystem, as well as significant contributions to global carbon and biogeochemical cycles. Given the importance of this symbiosis to the coral-algal holobiont and the reef ecosystem, understanding the mechanisms governing the establishment and long term maintenance of this symbiosis is essential. The overall aim of this project is to identify the mechanisms and selective processes that lead to the final assemblage of symbionts harbored by adult hosts. This question will be approached from two perspectives, ecologic and genomic, with the specific aims of determining (1) if different Symbiodinium strains differentially affect fitness of corals as the adult settles into a mature symbiosis (2) if competition among symbionts or environmental conditions contribute to the final host-symbiont pairing and (3) how host/symbiont transcriptomes varying as the symbiont community within a host is winnowed to the final assemblage found in the adult host. Traits that directly affect coral fitness (i.e. growth, survivorship, energy production) will be measured under different environmental conditions over the ontogeny of coral recruits that are experimentally infected with different types of Symbiodinium. Concurrently, high throughput gene expression profiling will be used to follow changes in gene expression between host and symbiont. Together, these data will be used to validate or falsify the hypotheses that the final symbiont assemblage found in the adult host is determined by (a) host selection (b) competition among symbionts and/or (c) environmental condition.</p>
<p>This study pools the expertise of two labs that have focused on these aspects of the symbiosis. The Coffroth lab pioneered the studies on early ontogeny of the symbiosis and symbiont diversity and will continue to take the lead in the ecological studies. The Medina lab is at the forefront in the development and utilization of genomic technology to study transcriptomic changes during the establishment and breakdown of the symbiosis. Furthermore, the Medina lab has the coral microarrays to be used in this study and in 2009 will also have oligo arrays for two Symbiodinium species based on 454 EST data. Although several groups have initial studies of the host transcriptome, none have combined an approach that examines the host and the symbiont in a single experiment. This will be a powerful approach as it will allow the investigators to track complementary changes in gene expression between host and symbiont and relate those to turnover in the symbiont community as the final symbiont complement is established.</p>
<p>The data resulting form the study will bridge an important gap in our understanding of the establishment and maintenance of coral-Symbiodinium symbiosis. Understanding the mechanism(s) regulating the establishment of the symbiosis will broaden our knowledge and help to predict the response of this symbiosis to future climate conditions. As in the past, the genomic tools (arrays, ESTs) will be made readily available to researchers via array distribution at cost, microarray analysis training, or sequence data, providing valuable resources to continue exploring these systems.</p>
<p>In conjunction the Aquarium of Niagara, Coffroth will develop educational and outreach programs to train and disseminate information on coral reefs to local area teachers and the general public. The Medina lab will continue to produce science and environment podcasts in multiple languages (English, Spanish and Hmong) with undergraduate students at UC Merced and will continue to collaborate with the California Academy of Sciences (CAS) in their coral reef outreach efforts. Additionally, this work will result in the training and mentoring of a postdoctoral fellow, at least one graduate student and at least 2 undergraduates. Through this project these students will have the opportunity to participate in research in both a lab and field setting, learning a range of ecological, molecular and algal culturing techniques. The extensive culture collection housed at the University at Buffalo is an important resource that is available to researchers worldwide which the proposed funding will help to maintain. Our EST annotations are publicly available through our EST database (<a href="http://montastraea.psu.edu/SymBioSys/" target="_blank">http://montastraea.psu.edu/SymBioSys/</a>).</p>
SymBioSys
largerWorkCitation
project
eng; USA
biota
oceans
coral reefs in Mexico, Panama, Florida Keys
2016-02-01
Florida Keys, Bahamas, Panama, Mexico
0
BCO-DMO catalogue of parameters from cDNA expressed sequence tags for the corals Acropora palmate and Orbicella faveola in Mexico, Panama, and the Florida Keys in 2003 (SymBioSys 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/637618.rdf
Name: species
Units: unitless
Description: <p>coral species</p>
http://lod.bco-dmo.org/id/dataset-parameter/637619.rdf
Name: experiment
Units: unitless
Description: <p>description of experiment</p>
http://lod.bco-dmo.org/id/dataset-parameter/637620.rdf
Name: molecule_type
Units: unitless
Description: <p>type of molecule that was sequenced: mRNA</p>
http://lod.bco-dmo.org/id/dataset-parameter/637621.rdf
Name: lat_PMor_Mex
Units: unitless
Description: <p>Puerto Morelos, Mexico latitude; north is postive</p>
http://lod.bco-dmo.org/id/dataset-parameter/637622.rdf
Name: lon_PMor_Mex
Units: unitless
Description: <p>Puerto Morelos, Mexico longitude; east is postive</p>
http://lod.bco-dmo.org/id/dataset-parameter/637623.rdf
Name: lat_KLar_FL
Units: unitless
Description: <p>Key Largo, Florida latitude; north is postive</p>
http://lod.bco-dmo.org/id/dataset-parameter/637624.rdf
Name: lon_KLar_FL
Units: unitless
Description: <p>Key Largo, Florida longitude; east is postive</p>
http://lod.bco-dmo.org/id/dataset-parameter/637625.rdf
Name: lat_CZap_Pan
Units: unitless
Description: <p>Cayos Zapatillas, Panama latitude; north is postive</p>
http://lod.bco-dmo.org/id/dataset-parameter/637626.rdf
Name: lon_CZap_Pan
Units: unitless
Description: <p>Cayos Zapatillas, Panama longitude; east is postive</p>
http://lod.bco-dmo.org/id/dataset-parameter/637627.rdf
Name: lat_ISol_Pan
Units: unitless
Description: <p>Isla Solarte, Panama latitude; north is postive</p>
http://lod.bco-dmo.org/id/dataset-parameter/637628.rdf
Name: lon_ISol_Pan
Units: unitless
Description: <p>Isla Solarte, Panama longitude; east is postive</p>
http://lod.bco-dmo.org/id/dataset-parameter/637629.rdf
Name: lat_CraK_Pan
Units: unitless
Description: <p>Cayos Zapatillas, Panama latitude; north is postive</p>
http://lod.bco-dmo.org/id/dataset-parameter/637630.rdf
Name: lon_CraK_Pan
Units: unitless
Description: <p>Cayos Zapatillas, Panama longitude; east is postive</p>
http://lod.bco-dmo.org/id/dataset-parameter/637631.rdf
Name: comment
Units: unitless
Description: <p>comments</p>
http://lod.bco-dmo.org/id/dataset-parameter/637632.rdf
Name: GenBank_GI
Units: unitless
Description: <p>linked accession number of the EST runs deposited at NCBI; a gi number (genInfo identifier) is a unique integer which identifies a particular sequence; the gi number will change every time the sequence changes.</p>
http://lod.bco-dmo.org/id/dataset-parameter/637633.rdf
Name: GenBank_ACC
Units: unitless
Description: <p>GenBank accession number</p>
http://lod.bco-dmo.org/id/dataset-parameter/637634.rdf
Name: EST_Name
Units: unitless
Description: <p>identifier of the Expressed Sequence Tags</p>
http://lod.bco-dmo.org/id/dataset-parameter/637635.rdf
Name: direction_seq
Units: unitless
Description: <p>sequencing direction: 5 is 5' and 3 is 3'</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
20426535
https://datadocs.bco-dmo.org/file/QAAXxVqikRZ8rN/EST_accnums.csv
EST_accnums.csv
Primary data file for dataset ID 627996
download
https://osprey.bco-dmo.org/dataset/627996/data/download
download
onLine
dataset
<p>Coral spawn and adult fragments were collected in the Florida Keys in a shallow reef environment at 30 ft. by scuba. RNA was extracted following standard protocols from Ambion kits. Samples were QCed with Nanodrop and Bionalyzer instruments and cDNA libraries were built for EST sequencing.</p>
<p><strong>Protocols:</strong><br />
<a href="http://dmoserv3.bco-dmo.org/data_docs/SymBioSys/Coral-RNA-isolation-protocol-for-small-preps-in-1.5mL-or-2mL-tubes.pdf" target="_blank">Coral RNA isolation protocol (for small prep’s in 1.5mL or 2mL tubes)</a><br />
<a href="http://dmoserv3.bco-dmo.org/data_docs/SymBioSys/Coral-RNA-isolation-for-large-preps-in-15mL-Falcon-tubes.pdf" target="_blank">Coral RNA isolation (for large prep’s in 15mL Falcon tubes)</a></p>
Specified by the Principal Investigator(s)
<p>Raw sequence data have been submitted to NCBI.</p>
<p><strong>BCO-DMO Processing:</strong><br />
- added conventional header with dataset name, PI name, version date, reference information<br />
- renamed parameters to BCO-DMO standard<br />
- added species column and links to NCBI accessions were added to the EST accession numbers.<br />
- split lats and lon into separate columns<br />
- replaced spaces with underscores</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: 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.
PI Supplied Instrument Name: Instrument Name: Thermal Cycler Instrument Short Name:Thermal Cycler Instrument Description: A thermal cycler or "thermocycler" is a general term for a type of laboratory apparatus, commonly used for performing polymerase chain reaction (PCR), that is capable of repeatedly altering and maintaining specific temperatures for defined periods of time. The device has a thermal block with holes where tubes with the PCR reaction mixtures can be inserted. The cycler then raises and lowers the temperature of the block in discrete, pre-programmed steps. They can also be used to facilitate other temperature-sensitive reactions, including restriction enzyme digestion or rapid diagnostics.
(adapted from http://serc.carleton.edu/microbelife/research_methods/genomics/pcr.html)
Deployment: Medina_genomics
Medina_genomics
U_Cal-Merced
laboratory
Medina_genomics
Mónica Medina
University of California-Merced
U_Cal-Merced
laboratory