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Dataset Overview | National Centers for Environmental Information (NCEI)

Proteomic Signatures of Corals from Thermodynamic Reefs (NCEI Accession 0216077)

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In this work, I took a protein profiling approach known as iTRAQ approach to characterize and quantify the proteins synthesized by 12 experimental coral samples. Specifically, corals were collected from an upwelling site in the Luzon Strait ("Houbihu"; 21°56’18.01’’N, 120°44’45.54’’E) and a non-upwelling "control" site in the nearby Taiwan Strait ("Houwan"; 22°01'23.30"N, 120°41'18.29"E) and exposed to either highly variable (upwelling-simulating) or stable temperatures in the laboratory for seven days prior to sacrificing for protein analysis (the "Seriatopora hystrix variable temperature study" [SHVTS]). In this submission, I have uploaded the proofs of the manuscript describing the proteomic data (Mayfield in press Microorganisms), two RAW files (SHVTS-A & SHVTS-B for iTRAQ batches A & B, respectively), two MZML (open-access mass spectrometry data) files (SHVTS-A.mzml & SHVTS-B.mzml), two MZID files (SHVTS-A.mzid & SHVTS-B.mzid), and a tab-delineated file that describes which samples were labeled with which iTRAQ tag ("Mayfield online supplemental data file"). I have also uploaded the supplemental material that accompanies the Mayfield (in press) article since that is what readers interested in the specifics of the proteomic analysis pipeline should consult. The peak data were queried against a conceptually translated S. hystrix-Cladocopium dinoflagellate transcriptome described in Mayfield et al. (2016 Mol Ecol) and found here: http://symbiont.iis.sinica.edu.tw/s_hystrix/static/html/#stat. Please note that all proteomic data represent a mix of multiple organisms (namely the anthozoan host and the dinoflagellate endosymbionts that inhabit their gastrodermal cells). All data analysis was conducted with Proteome Discoverer (Thermo-Fisher Scientific).
  • Cite as: Mayfield, Anderson B.; Cooperative Institute for Marine and Atmospheric Studies, University of Miami; Atlantic Oceanographic and Meteorological Laboratory (AOML) (2020). Proteomic Signatures of Corals from Thermodynamic Reefs (NCEI Accession 0216077). [indicate subset used]. NOAA National Centers for Environmental Information. Dataset. https://www.ncei.noaa.gov/archive/accession/0216077. Accessed [date].
gov.noaa.nodc:0216077
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  • MZID
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Distributor NOAA National Centers for Environmental Information
+1-301-713-3277
NCEI.Info@noaa.gov
Dataset Point of Contact NOAA National Centers for Environmental Information
ncei.info@noaa.gov
Time Period 2010-05-14 to 2010-06-15
Spatial Bounding Box Coordinates
West: 120.68841
East: 120.74598
South: 21.93834
North: 22.02314
Spatial Coverage Map
General Documentation
Associated Resources
Publication Dates
  • publication: 2020-09-09
Data Presentation Form Digital table - digital representation of facts or figures systematically displayed, especially in columns
Dataset Progress Status Complete - production of the data has been completed
Historical archive - data has been stored in an offline storage facility
Data Update Frequency As needed
Supplemental Information
Submission Package ID: BELJ6L
Purpose These data were collected to better understand the cellular biology of thermo-tolerant corals (i.e., those that can tolerate wide fluctuations in temperature). For more details, please see the articles referenced in the data package and on my personal website: coralreefdiagnostics.com.
Use Limitations
  • accessLevel: Public
  • Distribution liability: NOAA and NCEI make no warranty, expressed or implied, regarding these data, nor does the fact of distribution constitute such a warranty. NOAA and NCEI cannot assume liability for any damages caused by any errors or omissions in these data. If appropriate, NCEI can only certify that the data it distributes are an authentic copy of the records that were accepted for inclusion in the NCEI archives.
Dataset Citation
  • Cite as: Mayfield, Anderson B.; Cooperative Institute for Marine and Atmospheric Studies, University of Miami; Atlantic Oceanographic and Meteorological Laboratory (AOML) (2020). Proteomic Signatures of Corals from Thermodynamic Reefs (NCEI Accession 0216077). [indicate subset used]. NOAA National Centers for Environmental Information. Dataset. https://www.ncei.noaa.gov/archive/accession/0216077. Accessed [date].
Cited Authors
Principal Investigators
Contributors
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Acknowledgments
  • Related Funding Agency: Friendly Bear Editorial Service
  • Related Funding Agency: MacArthur Foundation
Theme keywords NODC DATA TYPES THESAURUS NODC OBSERVATION TYPES THESAURUS WMO_CategoryCode
  • oceanography
CoRIS Discovery Thesaurus
  • Numeric Data Sets > Biology
CoRIS Theme Thesaurus
  • EARTH SCIENCE > Biosphere > Zoology > Corals > Reef Monitoring and Assessment > Molecular Genetic Analysis > Proteomic Analysis
  • EARTH SCIENCE > Biosphere > Zoology > Corals > Scleractinia (stony corals)
  • EARTH SCIENCE > Oceans > Coastal Processes > Coral Reefs
  • EARTH SCIENCE > Oceans > Marine Biology > Coral
Global Change Master Directory (GCMD) Science Keywords
Data Center keywords NODC COLLECTING INSTITUTION NAMES THESAURUS NODC SUBMITTING INSTITUTION NAMES THESAURUS Global Change Master Directory (GCMD) Data Center Keywords
Instrument keywords NODC INSTRUMENT TYPES THESAURUS Global Change Master Directory (GCMD) Instrument Keywords
Place keywords NODC SEA AREA NAMES THESAURUS CoRIS Place Thesaurus
  • COUNTRY/TERRITORY > Taiwan > Hengchung > Nanwan Bay (21N120E0008)
  • OCEAN BASIN > Pacific Ocean > Hengchung > Nanwan Bay (21N120E0008)
Global Change Master Directory (GCMD) Location Keywords
Keywords NCEI ACCESSION NUMBER
Use Constraints
  • Cite as: Mayfield, Anderson B.; Cooperative Institute for Marine and Atmospheric Studies, University of Miami; Atlantic Oceanographic and Meteorological Laboratory (AOML) (2020). Proteomic Signatures of Corals from Thermodynamic Reefs (NCEI Accession 0216077). [indicate subset used]. NOAA National Centers for Environmental Information. Dataset. https://www.ncei.noaa.gov/archive/accession/0216077. Accessed [date].
Access Constraints
  • Use liability: NOAA and NCEI cannot provide any warranty as to the accuracy, reliability, or completeness of furnished data. Users assume responsibility to determine the usability of these data. The user is responsible for the results of any application of this data for other than its intended purpose.
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  • 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.
Lineage information for: dataset
Processing Steps
  • 2020-09-09T12:46:25Z - NCEI Accession 0216077 v1.1 was published.
Output Datasets
Lineage information for: dataset
Processing Steps
  • Parameter or Variable: protein concentrations (measured); Units: ratio to control (unitless); Observation Category: laboratory analysis; Sampling Instrument: manual sampling (SCUBA); Sampling and Analyzing Method: The isobaric tags for relative and absolute (protein) quantification (iTRAQ) approach of Ross et al. (2004 Mol Cell Proteomics) was used to label 12 experimental coral protein samples and two internal control samples that were used to normalize for batch-to-batch variation. Since there are only eight iTRAQ labels at present, this signifies that only eight proteins can be analyzed simultaneously. Given that 12 proteins were analyzed herein, two iTRAQ batches ("A" and "B" in the supplemental Excel file) were required to process all samples (6 experimental samples+1 normalizer/control sample in each batch).; Data Quality Method: An exhaustive series of quality control analyses were undertaken; please consult the attached methods file. Briefly, we only considered proteins sequenced in multiple batches that contained the iTRAQ tag.
Acquisition Information (collection)
Instrument
  • mass spectrometer
  • swimmer/diver
Last Modified: 2023-05-14T12:21:31Z
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