{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST001645","ANALYSIS_ID":"AN002691","VERSION":"1","CREATED_ON":"January 12, 2021, 12:34 pm"},

"PROJECT":{"PROJECT_TITLE":"Intraspecific variation in polar and nonpolar metabolite profiles of a threatened Caribbean coral","PROJECT_TYPE":"intraspecific variability","PROJECT_SUMMARY":"This project aims to identify differences in metabolomic profiles among seven known, unique genotypes of the threatened staghorn coral Acropora cervicornis.","INSTITUTE":"University of Florida","DEPARTMENT":"Department of Fisheries and Aquatic Sciences","LABORATORY":"Patterson Lab","LAST_NAME":"Patterson","FIRST_NAME":"Joshua","ADDRESS":"Florida Aquarium Center for Conservation, 529 Estuary Shore Lane, Apollo Beach, FL 33572","EMAIL":"joshpatterson@ufl.edu","PHONE":"(813) 419-4917","FUNDING_SOURCE":"This study was funded by the University of Florida’s Southeast Center for Integrated Metabolomics through grant number U24DK097209 from the National Institute of Health’s Common Fund metabolomics program. Additional assistance was provided by the National High Magnetic Field Laboratory supported by National Science Foundation Cooperative Agreement No. DMR-1644779 and the State of Florida. Partial support was provided by USDA National Institute of Food and Agriculture HATCH Project [FLA-FOR-005902].","CONTRIBUTORS":"Joseph A. Henrya, Kathryn E. Lohr , Ram B. Khattri, Joy Guingab-Cagmat, Matthew E. Merritt, Timothy J. Garrett, and Joshua T. Patterson"},

"STUDY":{"STUDY_TITLE":"Variability in metabolomic profiles among unique genotypes of Acropora cervicornis (part -II)","STUDY_TYPE":"intraspecific variability","STUDY_SUMMARY":"This project aims to identify differences in metabolomic profiles among seven known, unique genotypes of the threatened staghorn coral Acropora cervicornis.","INSTITUTE":"University of Florida","DEPARTMENT":"SECIM","LAST_NAME":"Patterson","FIRST_NAME":"Joshua","ADDRESS":"Florida Aquarium Center for Conservation, 529 Estuary Shore Lane, Apollo Beach, FL 33572","EMAIL":"joshpatterson@ufl.edu","PHONE":"(813) 419-4917","NUM_GROUPS":"7","TOTAL_SUBJECTS":"41"},

"SUBJECT":{"SUBJECT_TYPE":"Other organism","SUBJECT_SPECIES":"Acropora cervicornis","TAXONOMY_ID":"6130","GENOTYPE_STRAIN":"U77, U44, U41, U25, K1, K2, K3"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"-",
"Sample ID":"U77_A1",
"Factors":{"Genotype":"U77"},
"Additional sample data":{"RAW_FILE_NAME":"U77_A1.raw"}
},
{
"Subject ID":"-",
"Sample ID":"U77_A2",
"Factors":{"Genotype":"U77"},
"Additional sample data":{"RAW_FILE_NAME":"U77_A2.raw"}
},
{
"Subject ID":"-",
"Sample ID":"U77_B1",
"Factors":{"Genotype":"U77"},
"Additional sample data":{"RAW_FILE_NAME":"U77_B1.raw"}
},
{
"Subject ID":"-",
"Sample ID":"U77_B2",
"Factors":{"Genotype":"U77"},
"Additional sample data":{"RAW_FILE_NAME":"U77_B2.raw"}
},
{
"Subject ID":"-",
"Sample ID":"U77_C1",
"Factors":{"Genotype":"U77"},
"Additional sample data":{"RAW_FILE_NAME":"U77_C1.raw"}
},
{
"Subject ID":"-",
"Sample ID":"U77_C2",
"Factors":{"Genotype":"U77"},
"Additional sample data":{"RAW_FILE_NAME":"U77_C2.raw"}
},
{
"Subject ID":"-",
"Sample ID":"U44_A1",
"Factors":{"Genotype":"U44"},
"Additional sample data":{"RAW_FILE_NAME":"U44_A1.raw"}
},
{
"Subject ID":"-",
"Sample ID":"U44_A2",
"Factors":{"Genotype":"U44"},
"Additional sample data":{"RAW_FILE_NAME":"U44_A2.raw"}
},
{
"Subject ID":"-",
"Sample ID":"U44_B1",
"Factors":{"Genotype":"U44"},
"Additional sample data":{"RAW_FILE_NAME":"U44_B1.raw"}
},
{
"Subject ID":"-",
"Sample ID":"U44_B2",
"Factors":{"Genotype":"U44"},
"Additional sample data":{"RAW_FILE_NAME":"U44_B2.raw"}
},
{
"Subject ID":"-",
"Sample ID":"U44_C1",
"Factors":{"Genotype":"U44"},
"Additional sample data":{"RAW_FILE_NAME":"U44_C1.raw"}
},
{
"Subject ID":"-",
"Sample ID":"U44_C2",
"Factors":{"Genotype":"U44"},
"Additional sample data":{"RAW_FILE_NAME":"U44_C2.raw"}
},
{
"Subject ID":"-",
"Sample ID":"U41_A1",
"Factors":{"Genotype":"U41"},
"Additional sample data":{"RAW_FILE_NAME":"U41_A1.raw"}
},
{
"Subject ID":"-",
"Sample ID":"U41_A2",
"Factors":{"Genotype":"U41"},
"Additional sample data":{"RAW_FILE_NAME":"U41_A2.raw"}
},
{
"Subject ID":"-",
"Sample ID":"U41_B2",
"Factors":{"Genotype":"U41"},
"Additional sample data":{"RAW_FILE_NAME":"U41_B2.raw"}
},
{
"Subject ID":"-",
"Sample ID":"U41_C1",
"Factors":{"Genotype":"U41"},
"Additional sample data":{"RAW_FILE_NAME":"U41_C1.raw"}
},
{
"Subject ID":"-",
"Sample ID":"U41_C2",
"Factors":{"Genotype":"U41"},
"Additional sample data":{"RAW_FILE_NAME":"U41_C2.raw"}
},
{
"Subject ID":"-",
"Sample ID":"U25_A1",
"Factors":{"Genotype":"U25"},
"Additional sample data":{"RAW_FILE_NAME":"U25_A1.raw"}
},
{
"Subject ID":"-",
"Sample ID":"U25_A2",
"Factors":{"Genotype":"U25"},
"Additional sample data":{"RAW_FILE_NAME":"U25_A2.raw"}
},
{
"Subject ID":"-",
"Sample ID":"U25_B1",
"Factors":{"Genotype":"U25"},
"Additional sample data":{"RAW_FILE_NAME":"U25_B1.raw"}
},
{
"Subject ID":"-",
"Sample ID":"U25_B2",
"Factors":{"Genotype":"U25"},
"Additional sample data":{"RAW_FILE_NAME":"U25_B2.raw"}
},
{
"Subject ID":"-",
"Sample ID":"U25_C1",
"Factors":{"Genotype":"U25"},
"Additional sample data":{"RAW_FILE_NAME":"U25_C1.raw"}
},
{
"Subject ID":"-",
"Sample ID":"U25_C2",
"Factors":{"Genotype":"U25"},
"Additional sample data":{"RAW_FILE_NAME":"U25_C2.raw"}
},
{
"Subject ID":"-",
"Sample ID":"K1_A1",
"Factors":{"Genotype":"K1"},
"Additional sample data":{"RAW_FILE_NAME":"K1_A1.raw"}
},
{
"Subject ID":"-",
"Sample ID":"K1_A2",
"Factors":{"Genotype":"K1"},
"Additional sample data":{"RAW_FILE_NAME":"K1_A2.raw"}
},
{
"Subject ID":"-",
"Sample ID":"K1_B1",
"Factors":{"Genotype":"K1"},
"Additional sample data":{"RAW_FILE_NAME":"K1_B1.raw"}
},
{
"Subject ID":"-",
"Sample ID":"K1_B2",
"Factors":{"Genotype":"K1"},
"Additional sample data":{"RAW_FILE_NAME":"K1_B2.raw"}
},
{
"Subject ID":"-",
"Sample ID":"K1_C1",
"Factors":{"Genotype":"K1"},
"Additional sample data":{"RAW_FILE_NAME":"K1_C1.raw"}
},
{
"Subject ID":"-",
"Sample ID":"K1_C2",
"Factors":{"Genotype":"K1"},
"Additional sample data":{"RAW_FILE_NAME":"K1_C2.raw"}
},
{
"Subject ID":"-",
"Sample ID":"K2_A1",
"Factors":{"Genotype":"K2"},
"Additional sample data":{"RAW_FILE_NAME":"K2_A1.raw"}
},
{
"Subject ID":"-",
"Sample ID":"K2_A2",
"Factors":{"Genotype":"K2"},
"Additional sample data":{"RAW_FILE_NAME":"K2_A2.raw"}
},
{
"Subject ID":"-",
"Sample ID":"K2_B1",
"Factors":{"Genotype":"K2"},
"Additional sample data":{"RAW_FILE_NAME":"K2_B1.raw"}
},
{
"Subject ID":"-",
"Sample ID":"K2_B2",
"Factors":{"Genotype":"K2"},
"Additional sample data":{"RAW_FILE_NAME":"K2_B2.raw"}
},
{
"Subject ID":"-",
"Sample ID":"K2_C1",
"Factors":{"Genotype":"K2"},
"Additional sample data":{"RAW_FILE_NAME":"K2_C1.raw"}
},
{
"Subject ID":"-",
"Sample ID":"K2_C2",
"Factors":{"Genotype":"K2"},
"Additional sample data":{"RAW_FILE_NAME":"K2_C2.raw"}
},
{
"Subject ID":"-",
"Sample ID":"K3_A1",
"Factors":{"Genotype":"K3"},
"Additional sample data":{"RAW_FILE_NAME":"K3_A1.raw"}
},
{
"Subject ID":"-",
"Sample ID":"K3_A2",
"Factors":{"Genotype":"K3"},
"Additional sample data":{"RAW_FILE_NAME":"K3_A2.raw"}
},
{
"Subject ID":"-",
"Sample ID":"K3_B1",
"Factors":{"Genotype":"K3"},
"Additional sample data":{"RAW_FILE_NAME":"K3_B1.raw"}
},
{
"Subject ID":"-",
"Sample ID":"K3_B2",
"Factors":{"Genotype":"K3"},
"Additional sample data":{"RAW_FILE_NAME":"K3_B2.raw"}
},
{
"Subject ID":"-",
"Sample ID":"K3_C1",
"Factors":{"Genotype":"K3"},
"Additional sample data":{"RAW_FILE_NAME":"K3_C1.raw"}
},
{
"Subject ID":"-",
"Sample ID":"K3_C2",
"Factors":{"Genotype":"K3"},
"Additional sample data":{"RAW_FILE_NAME":"K3_C2.raw"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"Coral colonies were brought to the surface intact, and ~3 cm nubbins were clipped from actively growing branch tips. Nubbins were wrapped in aluminum foil and immediately frozen in liquid nitrogen. Nubbins were then ground down in an ice chilled mortar pastel in 10 mL of 2:1 Chloroform/Methanol solution. Supernatant was then transferred into a test tube labeled with sample I.D. and Organic and vortexed for 10 seconds. 2 mL of .9% NaCl was then added to each tube and vortexed for an additional 10 seconds. Samples were then allowed to separate for 15 minutes on ice. After the allotted time, the supernatant was separated and placed in a separate test tube labeled with sample I.D. and Aqueous. Both test tubes were then stored in a -80°C freezer until processing.","SAMPLE_TYPE":"Tissue and skeleton"},

"TREATMENT":{"TREATMENT_SUMMARY":"No treatment was applied; study was conducted on natural metabolomic variation among genotypes"},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"Metabolomic analyses were performed at the Southeast Center for Integrated Metabolomics (SECIM) at the University of Florida. Dried powder of aqueous phase samples acquired from methanol/chloroform extraction were dissolved in 50mM sodium phosphate buffer with 0.5mM D6-deuterated sodium trimethylsilylpropanesulfonate (DSS-d6). NMR spectra were measured using the first slice of a NOESY pulse sequence (tnnoesy) using 14.1 T Bruker Avance II NMR system with a CP TXI CryoProbe. The acquisition parameters used in Lohr et al. (2019) and Myer et al. (2020) were utilized to acquire proton spectra. All spectra were processed and the integrated area was extracted using MestReNova 11.0-17609 (Mestrelab Research S.L.). Before Fourier transformation, baseline correction and phase correction were applied with a line-broadening factor of 0.22 Hz and spectra were normalized with respect to a DSS signal at 0.0 ppm.","PROCESSING_METHOD":"Lyophilization and Homogenization","PROCESSING_STORAGE_CONDITIONS":"-80℃","EXTRACTION_METHOD":"Modified FOLCH extraction","EXTRACT_STORAGE":"-80℃","SAMPLE_RESUSPENSION":"In 50 mM phosphate buffer (pH 7.2) with 2 mM EDTA, 0.5 mM DSS and 0.2% sodium azide for aqueous phase samples.","SAMPLE_SPIKING":"0.5 mM of DSS for aqueous phase samples"},

"ANALYSIS":{"ANALYSIS_TYPE":"NMR","LABORATORY_NAME":"Matt","OPERATOR_NAME":"Ram Khattri","DETECTOR_TYPE":"Bruker","SOFTWARE_VERSION":"Bruker Topspin","ACQUISITION_DATE":"02/02/2018","DATA_FORMAT":"fid, 1r"},

"NM":{"INSTRUMENT_NAME":"Bruker Avance Neo 600 MHz/54mm console","INSTRUMENT_TYPE":"FT-NMR","NMR_EXPERIMENT_TYPE":"1D-1H","FIELD_FREQUENCY_LOCK":"Deuterium","STANDARD_CONCENTRATION":"0.5 mM DSS","SPECTROMETER_FREQUENCY":"600.2328273 MHz","NMR_PROBE":"CP TXI CryoProbe","NMR_SOLVENT":"Phosphate buffer (pH 7.2) + 2 mM EDTA + 0.5 mM DSS + 0.2% of sodium azide in deuterated environment","NMR_TUBE_SIZE":"1.5 mm O.D.","SHIMMING_METHOD":"Topshim","PULSE_SEQUENCE":"noesypr1d","WATER_SUPPRESSION":"presat","PULSE_WIDTH":"90-degree","RECEIVER_GAIN":"256","OFFSET_FREQUENCY":"2827.31 Hz","CHEMICAL_SHIFT_REF_CPD":"DSS (4,4-dimethyl-4-silapentane-1-sulfonic acid)","TEMPERATURE":"25 o C","NUMBER_OF_SCANS":"64","DUMMY_SCANS":"4","ACQUISITION_TIME":"4 s","RELAXATION_DELAY":"1 s","SPECTRAL_WIDTH":"7211.54","NUM_DATA_POINTS_ACQUIRED":"57690","REAL_DATA_POINTS":"65536","LINE_BROADENING":"0.22 Hz","ZERO_FILLING":"65,536 points","APODIZATION":"Exponential","BASELINE_CORRECTION_METHOD":"Spline","CHEMICAL_SHIFT_REF_STD":"0 ppm for DSS","BINNED_INCREMENT":"0.4ppm","BINNED_DATA_EXCLUDED_RANGE":"greater than 9.5 ppm and below 0.5 ppm including water regions","NMR_RESULTS_FILE":"ST001645_AN002691_Results.txt UNITS:ppm"}

}