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Results of cluster analysis and gene ontology: carbonate Organic Matrix (COM) proteins from coral, mollusk, and sea urchin; analyzed in the Falkowski lab at Rutgers from 2010-2014 (CROA project) (NCEI Accession 0277417)

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This dataset contains biological and survey - biological data collected at Rutgers_New_Brunswick during deployment lab_Falkowski at New Brunswick, NJ on 2014-10-29. These data include genus, species, and taxon. The instruments used to collect these data include Mass Spectrometer. These data were collected by Oscar M.E. Schofield, Paul G. Falkowski, Robert M. Sherrell, and Yair Rosenthal of Rutgers University as part of the "The Molecular Basis of Ocean Acidification Effects on Calcification in Zooxanthellate Corals (CROA)" project and "Science, Engineering and Education for Sustainability NSF-Wide Investment (SEES): Ocean Acidification (formerly CRI-OA) (SEES-OA)" program. The Biological and Chemical Oceanography Data Management Office (BCO-DMO) submitted these data to NCEI on 2023-01-23.

The following is the text of the dataset description provided by BCO-DMO:

Carbonate Organic Matrix (COM) proteins from coral, mollusk, and sea urchin.

Dataset Description:
Cluster analysis and gene ontology to compare ~1500 proteins, from over 100 studies, extracted from calcium carbonates in stony corals, bivalve and gastropod mollusks, and adult and larval sea urchins. This dataset includes information presented in Supplemental Table S2 from Drake et al. 2014. Refer to Drake et al. (2014) for more information on methodology and results.

Dataset Citation

Cite as: Falkowski, Paul G.; Rosenthal, Yair; Schofield, Oscar M.E.; Sherrell, Robert M. (2023). Results of cluster analysis and gene ontology: carbonate Organic Matrix (COM) proteins from coral, mollusk, and sea urchin; analyzed in the Falkowski lab at Rutgers from 2010-2014 (CROA project) (NCEI Accession 0277417). [indicate subset used]. NOAA National Centers for Environmental Information. Dataset. https://www.ncei.noaa.gov/archive/accession/0277417. Accessed [date].

Dataset Identifiers

ISO 19115-2 Metadata

gov.noaa.nodc:0277417

Full Text · XML

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	CSV TSV
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

Coverage Description	New Brunswick, NJ
Time Period	2014-10-29 to 2014-10-29
Spatial Bounding Box Coordinates	West: East: South: North:
Spatial Coverage Map

General Documentation

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Descriptive Information
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Associated Resources

Biological, chemical, physical, biogeochemical, ecological, environmental and other data collected from around the world during historical and contemporary periods of biological and chemical oceanographic exploration and research managed and submitted by the Biological and Chemical Oceanography Data Management Office (BCO-DMO)
- NCEI Collection
  Navigate directly to the URL for data access and direct download.
carbonate Organic Matrix (COM) proteins from coral, mollusk, and sea urchin; analyzed in the Falkowski lab at Rutgers from 2010-2014 (CROA project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2014-10-29. https://doi.org/10.26008/1912/bco-dmo.536485.1
- https://doi.org/10.26008/1912/bco-dmo.536485.1 (download)
  originator dataset

gov.noaa.nodc:BCO-DMO

Publication Dates	publication: 2023-04-03
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	Acquisition Description: Methodology described in Drake et al. 2014: Sequences from over 100 biomineral proteome studies were grouped by hierarchical clustering using the CD-HIT suite web server (Li and Godzik, 2006; Huang et al., 2010; http://weizhong-lab.ucsd.edu/cd-hit/ ) and assigned gene ontology (GO) terms using Blast2Go software (Conesa et al., 2005). Although 1531 proteins reduced to 1051 clusters at 30% similarity, only 64 clusters showed sequence similarity across phyla. Studies published from the 1990s through June 2013, using N-terminal and mass spectrometry COM sequencing, RT-PCR, or GO and KEGG annotation of genomic and transcriptomic data sets are included. Mass spectrometry sequences were excluded if the experimental data were compared with gene models from a different species. This dataset includes information presented in Supplemental Table S2 from Drake et al. 2014: Proteins from coral, mollusk, and sea urchin direct COM sequencing, RT-PCR, or GO and KEGG annotation. 1076 proteins, including redundancy when noted by multiple sources, reduced to 1031 non-redundant sequences.
Purpose	This dataset is available to the public for a wide variety of uses including scientific research and analysis.
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: Falkowski, Paul G.; Rosenthal, Yair; Schofield, Oscar M.E.; Sherrell, Robert M. (2023). Results of cluster analysis and gene ontology: carbonate Organic Matrix (COM) proteins from coral, mollusk, and sea urchin; analyzed in the Falkowski lab at Rutgers from 2010-2014 (CROA project) (NCEI Accession 0277417). [indicate subset used]. NOAA National Centers for Environmental Information. Dataset. https://www.ncei.noaa.gov/archive/accession/0277417. Accessed [date].
Cited Authors	Falkowski, Paul G. Rutgers University Rosenthal, Yair Rutgers University Schofield, Oscar M.E. Rutgers University Sherrell, Robert M. Rutgers University
Principal Investigators	Paul G. Falkowski Rutgers, The State University of New Jersey Yair Rosenthal Rutgers, The State University of New Jersey Oscar M.E. Schofield Rutgers, The State University of New Jersey Robert M. Sherrell Rutgers, The State University of New Jersey
Contributors	Rutgers, The State University of New Jersey
Resource Providers	Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Points of Contact	Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Publishers	NOAA National Centers for Environmental Information
Acknowledgments	Funding provided by NSF Emerging Frontiers Division (NSF EF) Award Number: EF-1041143 Award URL: http://nsf.gov/awardsearch/showAward?AWD_ID=1041143

Theme keywords	NODC DATA TYPES THESAURUS SPECIES IDENTIFICATION TAXONOMIC CODE NODC OBSERVATION TYPES THESAURUS biological survey - biological WMO_CategoryCode oceanography BCO-DMO Standard Parameters genus no standard parameter reference_paper species taxon Originator Parameter Names ID1 cluster_num detection_type genus group_num protein_name reference species taxon type
Data Center keywords	NODC COLLECTING INSTITUTION NAMES THESAURUS Rutgers, The State University of New Jersey NODC SUBMITTING INSTITUTION NAMES THESAURUS Biological and Chemical Oceanography Data Management Office Global Change Master Directory (GCMD) Data Center Keywords BCO-DMO > Biological and Chemical Oceanography Data Management Office
Platform keywords	BCO-DMO Platform Names Rutgers_New_Brunswick Global Change Master Directory (GCMD) Platform Keywords LABORATORY > LABORATORY
Instrument keywords	NODC INSTRUMENT TYPES THESAURUS mass spectrometer BCO-DMO Standard Instruments Mass Spectrometer Global Change Master Directory (GCMD) Instrument Keywords MASS SPECTROMETERS > MASS SPECTROMETERS Originator Instrument Names Mass Spec
Place keywords	Provider Place Names New Brunswick, NJ
Project keywords	BCO-DMO Standard Programs Science, Engineering and Education for Sustainability NSF-Wide Investment (SEES): Ocean Acidification (formerly CRI-OA) (SEES-OA) BCO-DMO Standard Projects The Molecular Basis of Ocean Acidification Effects on Calcification in Zooxanthellate Corals (CROA) Provider Deployment IDs lab_Falkowski Provider Funding Award Information Funding provided by NSF Emerging Frontiers Division (NSF EF) Award Number: EF-1041143
Keywords	NCEI ACCESSION NUMBER 0277417

Use Constraints	Cite as: Falkowski, Paul G.; Rosenthal, Yair; Schofield, Oscar M.E.; Sherrell, Robert M. (2023). Results of cluster analysis and gene ontology: carbonate Organic Matrix (COM) proteins from coral, mollusk, and sea urchin; analyzed in the Falkowski lab at Rutgers from 2010-2014 (CROA project) (NCEI Accession 0277417). [indicate subset used]. NOAA National Centers for Environmental Information. Dataset. https://www.ncei.noaa.gov/archive/accession/0277417. Accessed [date].
Data License	This dataset is licensed under a Creative Commons Attribution 4.0 International (CC BY 4.0) License. SPDX License: Creative Commons Attribution 4.0 International (CC-BY-4.0)
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	2023-04-03T12:34:12Z - NCEI Accession 0277417 v1.1 was published.
Output Datasets	NCEI Accession 0277417 v1.1 NCEI Accession 0277417 v1.1 (download) published 2023-04-03T12:34:12Z

Acquisition Information (collection)
Instrument	mass spectrometer

Last Modified: 2024-05-31T18:50:46Z
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Results of cluster analysis and gene ontology: carbonate Organic Matrix (COM) proteins from coral, mollusk, and sea urchin; analyzed in the Falkowski lab at Rutgers from 2010-2014 (CROA project) (NCEI Accession 0277417)

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