gov.noaa.nmfs.inport:73852 eng UTF8 dataset National Centers for Coastal Ocean Science resourceProvider NCCOS Scientific Data Coordinator NCCOS.data@noaa.gov nccos.data@noaa.gov pointOfContact 2026-03-04T19:17:27 ISO 19115-2 Geographic Information - Metadata Part 2 Extensions for imagery and gridded data ISO 19115-2:2009(E) NCCOS Assessment: Use of Omics to Support Coral Interventions: Proteomics of gametes collected from Acropora cervicornis, Acropora palmata, Orbicella faveolata to Optimize Sexual Reproduction in corals from Key Largo, FL, from 2022-08-13 to 2022-08-17, 2023-08-04 to 2023-08-05, and 2023-09-05 Proteomics of gametes collected from Acropora cervicornis, Acropora palmata, Orbicella faveolata creation revision 2024-11-12 publication NOAA/NMFS/EDM 73852 https://www.fisheries.noaa.gov/inport/item/73852 WWW:LINK-1.0-http--link Full Metadata Record View the complete metadata record on InPort for more information about this dataset. information Woodley, Cheryl M 843-762-8862 843-762-8737 331 Fort Johnson Road Charleston SC 29412 USA cheryl.woodley@noaa.gov principalInvestigator http://www.ebi.ac.uk/pride WWW:LINK-1.0-http--link Proteomics of gametes collected from Acropora cervicornis, Acropora palmata, Orbicella faveolata Project accession: PXD057823 [used placeholder url- need link directly to the resource] download This dataset is comprised of proteomics results to better understand gamete compatibility factors. The dataset includes gametes from three species, Acropora cervicornis, Acropora Palmata, Orbicella faveolate, which were collected in three locations near Key Largo, Florida (Ofav: Horseshoe Reef, Apal: North Dry Rocks, Acer: Carysfort) during three different time periods (August 2022, August 2023, and September 2023). Successful coral sexual reproduction is foundational to the achieving coral reef restoration, yet reproductive failure is a significant bottleneck to realizing restoration goals. The overall goal of this project is to identify factors that are involved in gamete compatibility and build on this knowledge to improve fertilization success and other downstream choke points in reproduction, such as larval settlement. The 2023 project was an extension of our previous work in genotype compatibility and kinship for Acropora cervicornis (Acer), Acropora palmata (Apal), and Orbicella faveolata (Ofav). The goals of this portion of the overall project were 1) in collaboration with the Drake Lab at the Medical University of South Carolina, we sought to identify glycans present in egg and sperm gametes across multiple genotypes and within three different coral species using Matrix Assisted Laser Desorption/Ionization (MALDI) imaging spectrometry, and 2) correlate the glycan expression with fertilization rates between egg and sperm gametes of the same species. completed NCCOS Scientific Data Coordinator NCCOS.data@noaa.gov nccos.data@noaa.gov custodian Acropora cervicornis Acropora palmata Orbicella faveolata theme World Register of Marine Species (WoRMS) CONTINENT > NORTH AMERICA > UNITED STATES OF AMERICA > FLORIDA CONTINENT > NORTH AMERICA > UNITED STATES OF AMERICA > FLORIDA > FLORIDA KEYS place Global Change Master Directory (GCMD) Location Keywords 20.8 Analytical Lab platform Global Change Master Directory (GCMD) Platform Keywords 17.2 Genetic Data Sets > Proteomic Analysis Numeric Data Sets > Biology theme CoRIS Discovery Thesaurus EARTH SCIENCE > Biosphere > Zoology > Corals > ESA Listed Species EARTH SCIENCE > Biosphere > Zoology > Corals > Reef Monitoring and Assessment > Molecular and Genetic Analysis > Proteomic Analysis EARTH SCIENCE > Biosphere > Zoology > Corals > Reproduction > Sexual Reproduction > Spawning theme CoRIS Theme Thesaurus NCCOS Research Priority > Coastal Change: Vulnerability, Mitigation, and Restoration NCCOS Research Topic > Restoration NCCOS Research Data Type > Laboratory Experiment NCCOS Research Location > Region > Atlantic Ocean NCCOS Research Location > U.S. States and Territories > Florida theme NCCOS Keywords COUNTRY/TERRITORY > United States of America > Florida > Dade County > Horseshoe Reef COUNTRY/TERRITORY > United States of America > Florida > Monroe County > Carysfort Reef COUNTRY/TERRITORY > United States of America > Florida > Monroe County > Dry Rocks place CoRIS Place Country/Territory Keywords OCEAN BASIN > Atlantic Ocean > North Atlantic Ocean > Florida Reef Tract > Biscayne Bay > Horseshoe Reef OCEAN BASIN > Atlantic Ocean > North Atlantic Ocean > Florida Reef Tract > Upper Florida Keys > Carysfort Reef OCEAN BASIN > Atlantic Ocean > North Atlantic Ocean > Florida Reef Tract > Upper Florida Keys > Dry Rocks place CoRIS Place Ocean/Seas Keywords DOC/NOAA/NOS/NCCOS > National Centers for Coastal Ocean Science, National Ocean Service, NOAA, U.S. Department of Commerce dataCentre Global Change Master Directory (GCMD) Data Center Keywords 2017-04-24 publication 8.5 Earth Science Data and Information System, Earth Science Projects Division, Goddard Space Flight Center (GSFC), National Aeronautics and Space Administration (NASA) https://forum.earthdata.nasa.gov/app.php/tag/GCMD%2BKeywords GCMD Keyword Forum Page Global Change Master Directory (GCMD). 2025. GCMD Keywords, Version 22. Greenbelt, MD: Earth Science Data and Information System, Earth Science Projects Division, Goddard Space Flight Center (GSFC), National Aeronautics and Space Administration (NASA). URL (GCMD Keyword Forum Page): https://forum.earthdata.nasa.gov/app.php/tag/GCMD+Keywords information custodian Coral Health and Disease Studies project InPort otherRestrictions Cite As: National Centers for Coastal Ocean Science, [Date of Access]: NCCOS Assessment: Use of Omics to Support Coral Interventions: Proteomics of gametes collected from Acropora cervicornis, Acropora palmata, Orbicella faveolata to Optimize Sexual Reproduction in corals from Key Largo, FL, from 2022-08-13 to 2022-08-17, 2023-08-04 to 2023-08-05, and 2023-09-05 [Data Date Range], https://www.fisheries.noaa.gov/inport/item/73852. NOAA provides no warranty, nor accepts any liability occurring from any incomplete, incorrect, or misleading data, or from any incorrect, incomplete, or misleading use of the data. It is the responsibility of the user to determine whether or not the data is suitable for the intended purpose. license These data were produced by NOAA and are not subject to copyright protection in the United States. NOAA waives any potential copyright and related rights in these data worldwide through the Creative Commons Zero 1.0 Universal Public Domain Dedication (CC0-1.0). SPDX License: Creative Commons Zero v1.0 Universal (CC0-1.0) otherRestrictions Access Constraints: Will become publicly available after publication of a peer-reviewed manuscript. otherRestrictions Use Constraints: None unclassified none none NOAA Data Management Plan (DMP) NOAA/NMFS/EDM 73852 https://www.fisheries.noaa.gov/inportserve/waf/noaa/nos/nccos/dmp/pdf/73852.pdf WWW:LINK-1.0-http--link NOAA Data Management Plan (DMP) NOAA Data Management Plan for this record on InPort. information crossReference eng; US oceans Sampling Instrument: Orbitrap Fusion Lumos LC-MS/MS Software: MaxQuant -80.294217 -80.211317 25.130967 25.2248 Reef Location Bounding Box where corals were originally sourced. Study time period 2022-08-13 2023-09-05 Methods: Egg and sperm gametes from three different coral species were collected from reefs around Key Largo during spawning season in August 2022 and August/September 2023. Fertilization trials were conducted within 3 hours after gamete collection. To our knowledge, this glycan imaging method has never before been used with coral gametes therefore, a significant amount of method development and trial and error was needed, which is defined in the specific methods sections. Fertilization trials: Fertilization trials were conducted by performing reciprocal crosses. Gamete bundles from a single coral genet were collected in a 15 mL tube and incubated at room temperature until bundles lyse. Sperm were transferred to a clean 15 mL tube without disrupting ova. Sperm were diluted and concentration was calculated using a cellometer. Sperm were diluted and added to the appropriate vials. Ova were washed with artificial sea water and added to the appropriate vials. The gametes were incubated together for 4-6 hours prior to fixing for counting. Gamete preservation. After gametes were combined for fertilization assays, the remaining sperm and ova were preserved for other molecular analyses. For glycan imaging, sperm and ova were fixed and stored at 4C until processing. Proteomic Analysis: Gametes from collected bundles were frozen at -20C in protein lysis buffer (5% SDS with protease inhibitor). The proteins were extracted by tip sonicating on ice and then centrifuged at 2,000 rcf for 5 minutes. The supernatant was transferred to a new tube and then centrifuged at 10,000 rcf for 10 minutes. The supernatant was transferred to a new tube and 50 ul was reserved for protein quantification. Protein was quantified using Pierce BCA Protein Assay Kit. Based on quantification, a volume equivalent to 100 ug was diluted to a volume of 80 ul in 5% SDS. Samples were reduced with 10 ul DTT at 60*C for 10 minutes. After cooling to room temperature (10 minutes), samples were alkylated with calcium acetamide and incubating in dark for 30 minutes. Alkylation was quenched by adding 12% phosphoric acid. Protein samples were digested following Protofi's S-trap protocol, using a 1:20 trypsin:sample ratio and incubating for 2 hours at 47C. The resulting peptides were evaporated until dry and resuspended in 100 ul 0.1% formic acid in water. Peptide concentration was quantified using Pierce Quantitative Fluorometric Peptide Assay kit. Peptides in solution were sent to University of Arkansas and analyzed using LC-MS/MS analysis. Peptide and proteins were identified using Mascot running against a known Orbicella faveolata annotated metagenome. Resulting search data was imported to Scaffold and identifications were accepted at <1% local FDR for peptides and proteins. Normalized spectral abundance factor was derived from normalized spectral counts and intensity based on absolute quantification (iBAQ) intensity data. XML (Structured Text) Zip National Institutes of Health, National Center for Biotechnology Information, Gene Expression Omnibus geo@ncbi.nlm.nih.gov https://www.ncbi.nlm.nih.gov/geo/ WWW:LINK-1.0-http--link Website Home Page Homepage for the organization. information Proteome Xchange http://www.ebi.ac.uk/pride Email: pride-support@ebi.ac.uk distributor https://www.ebi.ac.uk/pride/archive/projects/PXD057823 WWW:LINK-1.0-http--link Gamete Raw Data raw lc-ms/ms data download dataset Precision Gametes from three species of coral (Orbicella faveolata, Acropora cervicornis,and Acropora palmata) were collected across two spawning years (2022, 2023). Fertilization rates of reciprocal crosses (performed in triplicate) were compared with proteomics of individual gametes. These data were generated after collecting gametes spawned from Acropora palmata, Acorpora cervicornis, and Orbicella faveolata off the coast of Key Largo in August 2022 and August/September 2023. Fertilization trials were conducted by performing reciprocal crosses. Gamete bundles from a single coral genet were collected in a 15 mL tube and incubated at room temperature until bundles lyse. Sperm were transferred to a clean 15 mL tube without disrupting ova. Sperm were diluted and concentration was calculated using a cellometer. Sperm were diluted and added to the appropriate vials. Ova were washed with artificial sea water and added to the appropriate vials. The gametes were incubated together for 4-6 hours prior to fixing for counting. Saunders, Janet janet.saunders@noaa.gov processor After gametes were combined for fertilization assays, the remaining sperm and ova were preserved for other molecular analyses. For glycan imaging, sperm and ova were fixed and stored at 4*C until processing. Saunders, Janet janet.saunders@noaa.gov processor Gametes from collected bundles were frozen at -20*C in protein lysis buffer (5% SDS with protease inhibitor). The proteins were extracted by tip sonicating on ice and then centrifuged at 2,000 rcf for 5 minutes. The supernatant was transferred to a new tube and then centrifuged at 10,000 rcf for 10 minutes. The supernatant was transferred to a new tube and 50 ul was reserved for protein quantification. Protein was quantified using Pierce BCA Protein Assay Kit. Saunders, Janet janet.saunders@noaa.gov processor Based on quantification, a volume equivalent to 100 ug was diluted to a volume of 80 ul in 5% SDS. Samples were reduced with 10 ul DTT at 60*C for 10 minutes. After cooling to room temperature (10 minutes), samples were alkylated with calcium acetamide and incubating in dark for 30 minutes. Alkylation was quenched by adding 12% phosphoric acid. Protein samples were digested following Protofi's S-trap protocol, using a 1:20 trypsin:sample ratio and incubating for 2 hours at 47*C. The resulting peptides were evaporated until dry and resuspended in 100 ul 0.1% formic acid in water. Peptide concentration was quantified using Pierce Quantitative Fluorometric Peptide Assay kit. Saunders, Janet janet.saunders@noaa.gov processor Peptides in solution were sent to University of Arkansas and analyzed using LC-MS/MS analysis. Peptide and proteins were identified using Mascot running against a known Orbicella faveolata annotated metagenome. Resulting search data was imported to Scaffold and identifications were accepted at <1% local FDR for peptides and proteins. Normalized spectral abundance factor was derived from normalized spectral counts and intensity based on absolute quantification (iBAQ) intensity data. Saunders, Janet janet.saunders@noaa.gov processor Collection of gametes in Key Largo 2022 and 2023 Cheryl Woodley originator 2022 2023 otherRestrictions otherRestrictions Access Constraints: none | Use Constraints: none Orbitrap Fusion Lumos LC-MS/MS LC-MS/MS MaxQuant Software MaxQuant is a quantitative proteomics software package designed for analyzing large mass-spectrometric data sets. It is specifically aimed at high-resolution MS data. Several labeling techniques as well as label-free quantification are supported. Orbitrap Fusion Lumos LC-MS/MS LC-MS/MS