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-delimited 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).

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].

Dataset Identifiers

ISO 19115-2 Metadata

gov.noaa.nodc:0216077

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Download Data	HTTPS (download) Navigate directly to the URL for data access and direct download. FTP (download) 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).
Distribution Formats	XLSX ODS PDF MZID MZML RAW FA
Ordering Instructions	Contact NCEI for other distribution options and instructions.
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

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Descriptive Information
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Associated Resources

Proteomic signatures of corals from thermodynamic reefs
- Proteomic signatures of corals from thermodynamic reefs
  MassIVE Metadata Record
The effects of a variable temperature regime on the physiology of the reef-building coral Seriatopora hystrix: results from a laboratory-based reciprocal transplant
- The effects of a variable temperature regime on the physiology of the reef-building coral Seriatopora hystrix: results from a laboratory-based reciprocal transplant
  Mayfield, A.B., Chan, P.H., Putnam, H.P., Chen, C.S., Fan, T.Y. 2012. The effects of a variable temperature regime on the physiology of the reef-building coral Seriatopora hystrix: results from a laboratory-based reciprocal transplant. Journal of Experimental Biology 215: 4183-4195. https://doi.org/10.1242/jeb.071688
Mayfield, Anderson B. Proteomic Signatures of Corals from Thermodynamic Reefs; Microorganisms. 2020. https://doi.org/10.3390/microorganisms8081171
- https://doi.org/10.3390/microorganisms8081171
  NOAA Central Library: Journal Article

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	Mayfield, Anderson B. University of Miami (UM) Cooperative Institute for Marine and Atmospheric Studies, University of Miami Atlantic Oceanographic and Meteorological Laboratory (AOML)
Principal Investigators	Anderson B. Mayfield University of Miami (UM)
Contributors	University of Miami (UM)
Resource Providers	Anderson B. Mayfield US DOC; NOAA; OAR; Atlantic Oceanographic and Meteorological Laboratory (AOML) US DOC; NOAA; OAR; Atlantic Oceanographic and Meteorological Laboratory (AOML)
Publishers	NOAA National Centers for Environmental Information
Acknowledgments	Related Funding Agency: Friendly Bear Editorial Service Related Funding Agency: MacArthur Foundation

Theme keywords	NODC DATA TYPES THESAURUS CORAL ORGANIC CHEMICALS NODC OBSERVATION TYPES THESAURUS biological laboratory analyses 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 EARTH SCIENCE > OCEANS > OCEAN CHEMISTRY EARTH SCIENCE > SOLID EARTH > GEOMORPHIC LANDFORMS/PROCESSES > COASTAL LANDFORMS > CORAL REEFS
Data Center keywords	NODC COLLECTING INSTITUTION NAMES THESAURUS University of Miami NODC SUBMITTING INSTITUTION NAMES THESAURUS US DOC; NOAA; OAR; Atlantic Oceanographic and Meteorological Laboratory Global Change Master Directory (GCMD) Data Center Keywords DOC/NOAA/OAR/AOML > Atlantic Oceanographic and Meteorological Laboratory, OAR, NOAA, U.S. Department of Commerce
Instrument keywords	NODC INSTRUMENT TYPES THESAURUS mass spectrometer swimmer/diver Global Change Master Directory (GCMD) Instrument Keywords MASS SPECTROMETERS > MASS SPECTROMETERS
Place keywords	NODC SEA AREA NAMES THESAURUS South China Sea (Nan Hai) Taiwan Strait or Formosa Strait (T'ai-Wan Hai-Hsia) 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 OCEAN > PACIFIC OCEAN > NORTH PACIFIC OCEAN OCEAN > PACIFIC OCEAN > WESTERN PACIFIC OCEAN > SOUTH CHINA SEA
Keywords	NCEI ACCESSION NUMBER 0216077

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.
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.

Lineage information for: dataset
Processing Steps	2020-09-09T12:46:25Z - NCEI Accession 0216077 v1.1 was published.
Output Datasets	NCEI Accession 0216077 v1.1 NCEI Accession 0216077 v1.1 (download) published 2020-09-09T12:46:25Z

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.

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: 2024-04-19T13:46:41Z
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Proteomic Signatures of Corals from Thermodynamic Reefs (NCEI Accession 0216077)

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