{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST000134","ANALYSIS_ID":"AN000216","VERSION":"1","CREATED_ON":"08-08-2023"},

"PROJECT":{"PROJECT_TITLE":"Monitoring In Vitro Response of Selenium-Treated Prostate Cells by 1H NMR Spectroscopy","PROJECT_TYPE":"Metabolomics by 1H NMR","PROJECT_SUMMARY":"1H NMR data of prostate cells treated with selenium showed a decreasing trend in metabolite levels with the largest change exhibited by creatine mainly due to disrupted energy metabolism, and probably due to loss of structural integrity combined with external dissipation of metabolites. Lactate, choline-containing compounds, and glycine levels increased depending on the type of selenium used and the cell type. Principal component analysis (PCA) showed that SeM-treated cells can be distinguished from SeMSC-treated cells, and DU145 PCa from PNT1A normal cells.","INSTITUTE":"Purdue University","DEPARTMENT":"Biology/Chemistry","LABORATORY":"Biology/Chemistry Dept","LAST_NAME":"Isaac-Lam","FIRST_NAME":"Meden","ADDRESS":"1401 S US Hwy 421 Westville, Indiana USA","EMAIL":"isaaclam@pnc.edu","PHONE":"1-219-785-5776","FUNDING_SOURCE":"Indiana Academy of Science","DOI":"http://dx.doi.org/10.21228/M86C76"},

"STUDY":{"STUDY_TITLE":"Monitoring In Vitro Response of Selenium-Treated Prostate Cells by 1H NMR Spectroscopy","STUDY_TYPE":"Metabolite level response after treatment with organoselenium","STUDY_SUMMARY":"Metabolomics analysis was performed on DU145 prostate cancer cells and PNT1A non-tumorigenic prostate cells after treatment with selenomethionine and Se-methylselenocysteine using 800 MHz Bruker NMR spectrometer on 18 cell samples.","INSTITUTE":"Purdue University","DEPARTMENT":"Biology/Chemistry","LABORATORY":"Biology/Chemistry","LAST_NAME":"Isaac-Lam","FIRST_NAME":"Meden","ADDRESS":"1401 S US Hwy 421, Westville, IN 46391","EMAIL":"isaaclam@pnc.edu","PHONE":"219-785-5776","SUBMIT_DATE":"2015-01-13"},

"SUBJECT":{"SUBJECT_TYPE":"Human cells","SUBJECT_SPECIES":"Homo sapiens","TAXONOMY_ID":"9606","CELL_BIOSOURCE_OR_SUPPLIER":"ATCC, Sigma","CELL_STRAIN_DETAILS":"DU145 prostate cancer, PNT1A prostate nontumor","SUBJECT_COMMENTS":"10","CELL_PRIMARY_IMMORTALIZED":"Immortalized","CELL_PASSAGE_NUMBER":"10","CELL_COUNTS":"10","SPECIES_GROUP":"Human"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"-",
"Sample ID":"SeM (DU145)",
"Factors":{"Treatment":"SeM","Prostate Cell Line":"DU145"}
},
{
"Subject ID":"-",
"Sample ID":"SeM (PNT1A)",
"Factors":{"Treatment":"SeM","Prostate Cell Line":"PNT1A"}
},
{
"Subject ID":"-",
"Sample ID":"SeMSC (DU145)",
"Factors":{"Treatment":"SeMSC","Prostate Cell Line":"DU145"}
},
{
"Subject ID":"-",
"Sample ID":"SeMSC (PNT1A)",
"Factors":{"Treatment":"SeMSC","Prostate Cell Line":"PNT1A"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"After incubation for 24 hrs, cells were washed twice with 0.5 mL PBS in D2O (Cambridge Isotope Laboratories).  D2O (0.7 mL) was again added to each petri dish and cells were gently scraped from the surface with a sterile cell scraper. A volume of 0.7 mL of the harvested cell suspension was transferred into a 5 mm NMR tube and 10 mL of 100 mM TMSP in D2O was added to each tube.","SAMPLE_TYPE":"cell line","COLLECTION_METHOD":"scraping cells from flask","COLLECTION_LOCATION":"lab","COLLECTION_FREQUENCY":"once a week","VOLUMEORAMOUNT_COLLECTED":"0.7 mL per dish","STORAGE_CONDITIONS":"in ice","COLLECTION_TUBE_TEMP":"in ice"},

"TREATMENT":{"TREATMENT_SUMMARY":"Cells were grown to 80% confluence in Petri dishes (50 mm in diameter) in 4.5% CO2 at 37 OC for 5-6 days for full attachment to the substratum. After aspirating the old growth medium, 3 mL of SeM or SeMSC (300 mM) in fresh pre-warmed medium at 37 ºC was added to each dish.","TREATMENT_COMPOUND":"Selenomethionine / Se-methylselenocysteine","TREATMENT_DOSE":"300 mM","TREATMENT_DOSEVOLUME":"3 mL","TREATMENT_DOSEDURATION":"24 hrs","TREATMENT_VEHICLE":"dissolved in culture media","CELL_STORAGE":"incubator","CELL_GROWTH_CONTAINER":"petri dish (Corning)","CELL_GROWTH_CONFIG":"monolayer, adherent","CELL_GROWTH_RATE":"5-6 days","CELL_INOC_PROC":"trypsinized, then subculture","CELL_MEDIA":"RPMI, EMEM","CELL_ENVIR_COND":"37 C, 4.5% CO2 incubator","CELL_HARVESTING":"after trypsinization","CELL_PCT_CONFLUENCE":"80%","CELL_MEDIA_LASTCHANGED":"2-3 days"},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"Cells were grown to 80% confluence in Petri dishes (50 mm in diameter) in 4.5% CO2 at 37 OC for 5-6 days for full attachment to the substratum. After aspirating the old growth medium, 3 mL of SeM or SeMSC (300 mM) in fresh pre-warmed medium at 37 ºC was added to each dish. After incubation for 24 hrs, cells were washed twice with 0.5 mL PBS in D2O (Cambridge Isotope Laboratories).  D2O (0.7 mL) was again added to each petri dish and cells were gently scraped from the surface with a sterile cell scraper. A volume of 0.7 mL of the harvested cell suspension was transferred into a 5 mm NMR tube and 10 mL of 100 mM TMSP in D2O was added to each tube. Prior to NMR analysis, tubes were vortexed to ensure samples were in suspension. Control experiments using untreated cells were conducted in parallel with treated cells with the same incubation protocols and sample preparation.","SAMPLEPREP_PROTOCOL_FILENAME":"Prostate_Cells_Metabolomics_Procedure.doc","SAMPLE_RESUSPENSION":"in deuterated water","CELL_TYPE":"prostate"},

"CHROMATOGRAPHY":[],

"ANALYSIS":{"LABORATORY_NAME":"Purdue Chemistry NMR Facility","ANALYSIS_TYPE":"NMR","ACQUISITION_DATE":"May 30, 2014; June 6, 2014","SOFTWARE_VERSION":"AV-III-800","OPERATOR_NAME":"Dr. John Harwood","DETECTOR_TYPE":"TX1"},

"NM":{"INSTRUMENT_NAME":"Bruker Avance III","INSTRUMENT_TYPE":"FT-NMR","NMR_EXPERIMENT_TYPE":"1D 1H","FIELD_FREQUENCY_LOCK":"Deuterium","STANDARD_CONCENTRATION":"1.43 mM","SPECTROMETER_FREQUENCY":"800 MHz","NMR_PROBE":"TX1, inverse","NMR_SOLVENT":"D2O","NMR_TUBE_SIZE":"5 mm x 7 in","SHIMMING_METHOD":"gradient, topshim","PULSE_SEQUENCE":"zg one-pulse","WATER_SUPPRESSION":"presaturation","PULSE_WIDTH":"8.5 msec","POWER_LEVEL":"12.25 W","RECEIVER_GAIN":"912","OFFSET_FREQUENCY":"4.8 ppm","PRESATURATION_POWER_LEVEL":"57 dB","CHEMICAL_SHIFT_REF_CPD":"TMSP","TEMPERATURE":"295.9","NUMBER_OF_SCANS":"256","DUMMY_SCANS":"8","ACQUISITION_TIME":"1.4680564","RELAXATION_DELAY":"6.5 msec","SPECTRAL_WIDTH":"11160 Hz","NUM_DATA_POINTS_ACQUIRED":"32 K","REAL_DATA_POINTS":"32 K","LINE_BROADENING":"1 Hz","ZERO_FILLING":"16K","APODIZATION":"lorentzian","BASELINE_CORRECTION_METHOD":"polynomial","CHEMICAL_SHIFT_REF_STD":"TMSP"},

"NMR_METABOLITE_DATA":{
"Units":"% Relative change",

"Data":[{"Metabolite":"Alanine","SeM (DU145)":"-35.8000","SeM (PNT1A)":"-23.3000","SeMSC (DU145)":"-12.3000","SeMSC (PNT1A)":"-55.8000"},{"Metabolite":"b-Glucose","SeM (DU145)":"-37.3000","SeM (PNT1A)":"-60.8000","SeMSC (DU145)":"-28.9000","SeMSC (PNT1A)":"-64.0000"},{"Metabolite":"Choline","SeM (DU145)":"10.0000","SeM (PNT1A)":"-45.8000","SeMSC (DU145)":"-39.7000","SeMSC (PNT1A)":"-70.3000"},{"Metabolite":"Creatine","SeM (DU145)":"-25.0000","SeM (PNT1A)":"-56.1000","SeMSC (DU145)":"-35.4000","SeMSC (PNT1A)":"-80.7000"},{"Metabolite":"Glycerophosphocholine","SeM (DU145)":"5.4000","SeM (PNT1A)":"-33.3000","SeMSC (DU145)":"-35.2000","SeMSC (PNT1A)":"-58.3000"},{"Metabolite":"Glycine","SeM (DU145)":"-4.2000","SeM (PNT1A)":"25.4000","SeMSC (DU145)":"-17.5000","SeMSC (PNT1A)":"-57.5000"},{"Metabolite":"Lactate","SeM (DU145)":"11.4000","SeM (PNT1A)":"-25.9000","SeMSC (DU145)":"65.6000","SeMSC (PNT1A)":"-31.9000"},{"Metabolite":"Lipids","SeM (DU145)":"-28.3000","SeM (PNT1A)":"-56.1000","SeMSC (DU145)":"-54.9000","SeMSC (PNT1A)":"-75.4000"},{"Metabolite":"Nicotine adenine dinucleotide phosphate (NADP)","SeM (DU145)":"","SeM (PNT1A)":"-40.0000","SeMSC (DU145)":"-75.0000","SeMSC (PNT1A)":"-30.0000"},{"Metabolite":"Phosphocholine","SeM (DU145)":"-34.2000","SeM (PNT1A)":"-59.6000","SeMSC (DU145)":"-5.7000","SeMSC (PNT1A)":"-54.4000"},{"Metabolite":"Taurine","SeM (DU145)":"-14.8000","SeM (PNT1A)":"-10.9000","SeMSC (DU145)":"-29.0000","SeMSC (PNT1A)":"-19.2000"},{"Metabolite":"Uridine 2^-diphospate","SeM (DU145)":"","SeM (PNT1A)":"-33.3000","SeMSC (DU145)":"-35.2000","SeMSC (PNT1A)":"-61.1000"}],

"Metabolites":[{"Metabolite":"Alanine","pubchem_id":"5950","inchi_key":"","kegg_id":"C00041","other_id":"Ala","other_id_type":"IsaacLam_ID","ri":"","ri_type":"","moverz_quant":"","":""},{"Metabolite":"b-Glucose","pubchem_id":"","inchi_key":"","kegg_id":"","other_id":"b-Glc","other_id_type":"IsaacLam_ID","ri":"","ri_type":"","moverz_quant":"","":""},{"Metabolite":"Choline","pubchem_id":"305","inchi_key":"","kegg_id":"C00114","other_id":"Cho","other_id_type":"IsaacLam_ID","ri":"","ri_type":"","moverz_quant":"","":""},{"Metabolite":"Creatine","pubchem_id":"586","inchi_key":"","kegg_id":"C00300","other_id":"Cr","other_id_type":"IsaacLam_ID","ri":"","ri_type":"","moverz_quant":"","":""},{"Metabolite":"Glycerophosphocholine","pubchem_id":"657272","inchi_key":"","kegg_id":"","other_id":"GPC","other_id_type":"IsaacLam_ID","ri":"","ri_type":"","moverz_quant":"","":""},{"Metabolite":"Glycine","pubchem_id":"750","inchi_key":"","kegg_id":"C00037","other_id":"Gly","other_id_type":"IsaacLam_ID","ri":"","ri_type":"","moverz_quant":"","":""},{"Metabolite":"Lactate","pubchem_id":"107689","inchi_key":"","kegg_id":"C00186","other_id":"Lac","other_id_type":"IsaacLam_ID","ri":"","ri_type":"","moverz_quant":"","":""},{"Metabolite":"Lipids","pubchem_id":"","inchi_key":"","kegg_id":"","other_id":"Lipids","other_id_type":"IsaacLam_ID","ri":"","ri_type":"","moverz_quant":"","":""},{"Metabolite":"Nicotine adenine dinucleotide phosphate (NADP)","pubchem_id":"","inchi_key":"","kegg_id":"","other_id":"NADP","other_id_type":"IsaacLam_ID","ri":"","ri_type":"","moverz_quant":"","":""},{"Metabolite":"Phosphocholine","pubchem_id":"135437","inchi_key":"","kegg_id":"","other_id":"PC","other_id_type":"IsaacLam_ID","ri":"","ri_type":"","moverz_quant":"","":""},{"Metabolite":"Taurine","pubchem_id":"1123","inchi_key":"","kegg_id":"C00245","other_id":"Tau","other_id_type":"IsaacLam_ID","ri":"","ri_type":"","moverz_quant":"","":""},{"Metabolite":"Uridine 2'-diphospate","pubchem_id":"","inchi_key":"","kegg_id":"","other_id":"UDP","other_id_type":"IsaacLam_ID","ri":"","ri_type":"","moverz_quant":"","":""}]
}

}