Dataset: Coral cDNA Expressed Sequences
Deployment: Medina_genomics

cDNA Expressed Sequence Tags for the corals Acropora palmate and Orbicella faveola

Principal Investigator:

Mónica Medina (University of California-Merced, UC Merced)

BCO-DMO Data Manager:

Nancy Copley (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Project:

Ontogenic change in Cnidarian-algal symbioses: A genomic and ecologic perspective (SymBioSys)

Current State:

Final no updates expected

Version:

2016-02-01

Version Date:

2016-02-01

Data URL:

https://osprey.bco-dmo.org/dataset-deployment/637650/data

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Description

This dataset includes links to NCBI accession pages for cDNA EST's for the corals Acropora palmate and Orbicella faveola (Montastraea faveolata).

Related References:

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 Montastraea faveolata. Molecular Ecology, doi: 10.1111/j.1365-294X.2008.03879.x

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

DeSalvo MK., S Sunagawa, CR. Voolstra, M. Medina (2010) Transcriptomic responses to heat stress and bleaching in the elkhorn coral Acropora palmate. Mar Ecol Prog Ser, 402: 97–113, doi: 10.3354/meps08372

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.

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, Acropora palmata and Montastraea faveolata. BMC Genomics, 9:97, doi:10.1186/1471-2164-9-97.

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. Molecular Ecology, 18, 1823–1833, doi: 10.1111/j.1365-294X.2009.04167.x

Methods & Sampling

Dataset acquisition description

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.

Protocols:
Coral RNA isolation protocol (for small prep’s in 1.5mL or 2mL tubes)
Coral RNA isolation (for large prep’s in 15mL Falcon tubes)

Data Processing Description

Dataset Processing Description

Raw sequence data have been submitted to NCBI.

BCO-DMO Processing:
- added conventional header with dataset name, PI name, version date, reference information
- renamed parameters to BCO-DMO standard
- added species column and links to NCBI accessions were added to the EST accession numbers.
- split lats and lon into separate columns
- replaced spaces with underscores

More information about this dataset deployment

Funding

Award Number	Funding Source
OCE-0926906	NSF Division of Ocean Sciences

Instruments

Automated DNA Sequencer

Supplied Name:

Supplied Description:

Instrument Type

Generic Name: Automated DNA Sequencer

Acronym: Automated Sequencer

Generic Description:

General term for a laboratory instrument used for deciphering the order of bases in a strand of DNA. Sanger sequencers detect fluorescence from different dyes that are used to identify the A, C, G, and T extension reactions. Contemporary or Pyrosequencer methods are based on detecting the activity of DNA polymerase (a DNA synthesizing enzyme) with another chemoluminescent enzyme. Essentially, the method allows sequencing of a single strand of DNA by synthesizing the complementary strand along it, one base pair at a time, and detecting which base was actually added at each step.

Thermal Cycler

Supplied Name:

Supplied Description:

Instrument Type

Generic Name: Thermal Cycler

Generic 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)

Parameters

Supplied Name	Supplied description	Supplied Units	Standard Name
species	coral species	unitless	species
experiment	description of experiment	unitless	brief_desc
molecule_type	type of molecule that was sequenced: mRNA	unitless	no_bcodmo_term
lat_PMor_Mex	Puerto Morelos, Mexico latitude; north is postive	unitless	lat
lon_PMor_Mex	Puerto Morelos, Mexico longitude; east is postive	unitless	lon
lat_KLar_FL	Key Largo, Florida latitude; north is postive	unitless	lat
lon_KLar_FL	Key Largo, Florida longitude; east is postive	unitless	lon
lat_CZap_Pan	Cayos Zapatillas, Panama latitude; north is postive	unitless	lat
lon_CZap_Pan	Cayos Zapatillas, Panama longitude; east is postive	unitless	lon
lat_ISol_Pan	Isla Solarte, Panama latitude; north is postive	unitless	lat
lon_ISol_Pan	Isla Solarte, Panama longitude; east is postive	unitless	lon
lat_CraK_Pan	Cayos Zapatillas, Panama latitude; north is postive	unitless	lat
lon_CraK_Pan	Cayos Zapatillas, Panama longitude; east is postive	unitless	lon
comment	comments	unitless	comment
GenBank_GI	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.	unitless	accession_number
GenBank_ACC	GenBank accession number	unitless	accession_number
EST_Name	identifier of the Expressed Sequence Tags	unitless	accession_number
direction_seq	sequencing direction: 5 is 5' and 3 is 3'	unitless	no_bcodmo_term

Database

Contribute Data

Dataset: Coral cDNA Expressed Sequences
Deployment: Medina_genomics

Dataset acquisition description

Dataset Processing Description

Database

Contribute Data

Dataset: Coral cDNA Expressed SequencesDeployment: Medina_genomics

Dataset acquisition description

Dataset Processing Description

Dataset: Coral cDNA Expressed Sequences
Deployment: Medina_genomics