Differential proteomic analysis of the massive star coral Orbicella faveolata exposed to experimentally elevated temperatures (NCEI Accession 0242879)
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title: Differential proteomic analysis of the massive star coral Orbicella faveolata exposed to experimentally elevated temperatures (NCEI Accession 0242879)
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abstract: An inshore-to-offshore gradient in reef coral resilience to high temperatures exists in the Upper Florida Keys, with massive corals of the highly turbid nearshore reefs demonstrating higher capacity to resist summer bleaching than offshore conspecifics. After corroborating this trend with diverse Orbicella faveolata genotypes exposed to elevated temperatures in the laboratory, a proteomic analysis was taken with a subset of 20 samples via iTRAQ labeling followed by nano-liquid chromatography+mass spectrometry; 46 host coral and 40 Symbiodiniaceae dinoflagellate proteins passed all stringent quality control criteria, and the partial proteomes of biopsies of 1) healthy controls, 2) sub-lethally-stressed samples, and 3) actively bleaching corals differed significantly from one another. The proteomic data were then used to train predictive models of coral colony bleaching susceptibility, and both generalized multivariate regression and neural network models were capable of doing so with 100% accuracy. Successful future testing of the predictive power of these models in situ will establish the capacity to monitor coral health on a proactive, pre-death timescale.
purpose: These proteomic (i.e., protein concentration) data were collected in order to better understand the molecular basis of resilience to rising seawater temperatures in replicate genotypes of the framework-building Caribbean coral Orbicella faveolata collected from several reef sites within the upper Florida Keys (see appended documents for permitting information, coordinates, and other supporting meta-data).
credit: Related Funding Agency: National Oceanic and Atmospheric Administration
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address: (CI_Address)
electronicMailAddress: NCEI.Info@noaa.gov
role: (CI_RoleCode) pointOfContact
distributionOrderProcess: (MD_StandardOrderProcess)
fees: In most cases, electronic downloads of the data are free. However, fees may apply for custom orders, data certifications, copies of analog materials, and data distribution on physical media.
orderingInstructions: Contact NCEI for other distribution options and instructions.
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onLine: (CI_OnlineResource)
linkage: https://www.ncei.noaa.gov/archive/accession/0242879
protocol: HTTPS
applicationProfile: Web browser
name: NCEI Dataset Landing Page
description: Navigate directly to the URL for a descriptive web page with download links.
function: (CI_OnLineFunctionCode) information
onLine: (CI_OnlineResource)
linkage: https://www.ncei.noaa.gov/archive/accession/oas/242879
protocol: HTTPS
applicationProfile: Web browser
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function: (CI_OnLineFunctionCode) information
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linkage: https://www.ncei.noaa.gov/archive/accession/download/242879
protocol: HTTPS
applicationProfile: Web browser
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function: (CI_OnLineFunctionCode) download
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linkage: ftp://ftp-oceans.ncei.noaa.gov/nodc/archive/arc0191/0242879/
protocol: FTP
applicationProfile: Any FTP client
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description: These data are available through the File Transfer Protocol (FTP). FTP is no longer supported by most internet browsers. You may copy and paste the FTP link to the data into an FTP client (e.g., FileZilla or WinSCP).
function: (CI_OnLineFunctionCode) download
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dataQualityInfo: (DQ_DataQuality)
scope: (DQ_Scope)
level: (MD_ScopeCode) dataset
lineage: (LI_Lineage)
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description: NCEI Accession 0242879 v1.1 was published.
dateTime:
DateTime: 2021-12-06T21:45:08Z
output: (LE_Source)
sourceCitation: (CI_Citation)
title: NCEI Accession 0242879 v1.1
date: (CI_Date)
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onlineResource: (CI_OnlineResource)
linkage: https://www.ncei.noaa.gov/archive/accession/0242879/1.1
protocol: HTTPS
name: NCEI Accession 0242879 v1.1
description: published 2021-12-06T21:45:08Z
function: (CI_OnLineFunctionCode) download
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dataQualityInfo: (DQ_DataQuality)
scope: (DQ_Scope)
level: (MD_ScopeCode) dataset
lineage: (LI_Lineage)
processStep: (LE_ProcessStep)
description: Parameter or Variable: protein concentration (measured); Units: ratio to control sample; Observation Category: laboratory analysis; Sampling Instrument: Q Exactive mass spectrometer; Sampling and Analyzing Method: Corals were sampled from multiple reefs in the Florida Keys National Marine Sanctuary, cored, and used in laboratory experiments. Upon sampling, proteins were extracted, labeled using iTRAQ technology (Sciex, USA) and analyzed via mass spectrometry. Please see the accompanying documents for methodological details.; Data Quality Method: Proteins were quantified using a standard BCA assay and assessed for quality via gel electrophoresis (SDS-PAGE; see accompanying Word documents for details.)..
processStep: (LE_ProcessStep)
description: Parameter or Variable: protein sequences (measured); Units: amino acids; Observation Category: laboratory analysis; Sampling Instrument: Q Exactive mass spectrometer; Sampling and Analyzing Method: Please see documents "Mayfield OFAV iTRAQ methods" and "Mayfield OFAV iTRAQ appendix" for details.; Data Quality Method: Please see documents "Mayfield OFAV iTRAQ methods" and "Mayfield OFAV iTRAQ appendix" for details..
processStep: (LE_ProcessStep)
description: Parameter or Variable: predictive model (calculated); Units: coral bleaching susceptibility (probability); Observation Category: model output; Sampling Instrument: not applicable; Sampling and Analyzing Method: Please see documents "Mayfield OFAV iTRAQ methods" and "Mayfield OFAV iTRAQ appendix" for details.; Data Quality Method: Please see documents "Mayfield OFAV iTRAQ methods" and "Mayfield OFAV iTRAQ appendix" for details..
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metadataMaintenance: (MD_MaintenanceInformation)
maintenanceAndUpdateFrequency: (MD_MaintenanceFrequencyCode) asNeeded
maintenanceNote: Metadata are developed, maintained and distributed by NCEI. Updates are performed as needed to maintain currentness.
contact: (CI_ResponsibleParty)
organisationName: NOAA National Centers for Environmental Information
role: (CI_RoleCode) custodian
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acquisitionInformation: (MI_AcquisitionInformation)
instrument: (MI_Instrument)
identifier: (MD_Identifier)
code: mass spectrometer
type: mass spectrometer
description: Instrument that measure the massess and relative concentrations of atoms and molecules
