{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST000468","ANALYSIS_ID":"AN000731","VERSION":"1","CREATED_ON":"September 12, 2016, 2:48 pm"},

"PROJECT":{"PROJECT_TITLE":"Enterococcus faecalis nucleotie profiles","PROJECT_SUMMARY":"Determination of metabolite profile of E. faecalis OG1RF control as compared to exposure to mupirocin or decoyinine","INSTITUTE":"Univeristy of Florida","DEPARTMENT":"Oral Biology","LABORATORY":"Oral Biology Lemos-Abranches","LAST_NAME":"Lemos","FIRST_NAME":"Jose","ADDRESS":"1395 Center Drive, PO Box 100424 Gainesville, FL 32610","EMAIL":"jlemos@dental.ufl.edu","PHONE":"352-273-8843","FUNDING_SOURCE":"UF start-up funds"},

"STUDY":{"STUDY_TITLE":"Enterococcus faecalis nucleotide profiles following mupirocin or decoyinine","STUDY_TYPE":"Exposure to mupirocin or decoyinine","STUDY_SUMMARY":"Triplicate samples of E. faecalis OG1RF will be grown in FMC-AUG to OD600 = 0.25. The cultures will be split and exposed to DMSO, mupirocin (0.01mg/mL) or decoyinine (0.1mg/mL) for 15 minutes. 6E9 cells will be harvested by fast filtration, scraped off of membrane into ice-cold PBS, and pelleted by centrifugation, and stored at -80C until shipment.","INSTITUTE":"Univeristy of Florida","DEPARTMENT":"SECIM","LABORATORY":"Lemos-Abranches","LAST_NAME":"Kajfasz","FIRST_NAME":"Jessica","ADDRESS":"1395 Center Drive, PO Box 100424 Gainesville, FL 32610","EMAIL":"jkajfasz@dental.ufl.edu","PHONE":"352-273-6675","NUM_GROUPS":"3","TOTAL_SUBJECTS":"9"},

"SUBJECT":{"SUBJECT_TYPE":"Bacterial cells","SUBJECT_SPECIES":"Enterococcus faecalis","TAXONOMY_ID":"1351","GENOTYPE_STRAIN":"OG1RF"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"1 DMSO",
"Sample ID":"OG1RF_1 DMSO",
"Factors":{"Exposure":"DMSO"}
},
{
"Subject ID":"2 DMSO",
"Sample ID":"OG1RF_2 DMSO",
"Factors":{"Exposure":"DMSO"}
},
{
"Subject ID":"3 DMSO",
"Sample ID":"OG1RF_3 DMSO",
"Factors":{"Exposure":"DMSO"}
},
{
"Subject ID":"1 Mup",
"Sample ID":"OG1RF_1 Mup",
"Factors":{"Exposure":"Mupirocin, 0.01mg/mL"}
},
{
"Subject ID":"2 Mup",
"Sample ID":"OG1RF_2 Mup",
"Factors":{"Exposure":"Mupirocin, 0.01mg/mL"}
},
{
"Subject ID":"3 Mup",
"Sample ID":"OG1RF_3 Mup",
"Factors":{"Exposure":"Mupirocin, 0.01mg/mL"}
},
{
"Subject ID":"1 Decoy",
"Sample ID":"OG1RF_1 Decoy",
"Factors":{"Exposure":"Decoyinine, 0.1mg/mL"}
},
{
"Subject ID":"2 Decoy",
"Sample ID":"OG1RF_2 Decoy",
"Factors":{"Exposure":"Decoyinine, 0.1mg/mL"}
},
{
"Subject ID":"3 Decoy",
"Sample ID":"OG1RF_3 Decoy",
"Factors":{"Exposure":"Decoyinine, 0.1mg/mL"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"After the 15 minute treatment interval, 20mL sample will be harvested by filtration onto 0.45uM nitrocellulose membrane. The cells will be scraped off of the membrane into ice-cold PBS (~1mL), centrifuged for 45 seconds at 12K RPM, liquid aspirated and stored at -80C until sending for analysis.","SAMPLE_TYPE":"Bacterial cells","COLLECTION_METHOD":"Fast filtration","VOLUMEORAMOUNT_COLLECTED":"20ml","STORAGE_CONDITIONS":"-80C"},

"TREATMENT":{"TREATMENT_SUMMARY":"Triplicate cultures of E. faecalis OG1RF will be grown in FMC-AUG to OD600 = 0.25. The cultures will be split into 3 equal volumes of 30mL which will be exposed to 100uL DMSO, 0.01mg/mL mupirocin, or 0.1mg/mL decoyinine for 15 minutes. At this point, 10mL sample will be removed for protein analysis. The remaining 20mL will be harvested by fast filtration for analysis.|Triplicate cultures of E. faecalis OG1RF will be grown in FMC-AUG to OD600 = 0.25. The cultures will be split into 3 equal volumes of 30mL which will be exposed to 100uL DMSO, 0.01mg/mL mupirocin, or 0.1mg/mL decoyinine for 15 minutes. At this point, 10mL sample will be removed for protein analysis. The remaining 20mL will be harvested by fast filtration for analysis.|Triplicate cultures of E. faecalis OG1RF will be grown in FMC-AUG to OD600 = 0.25. The cultures will be split into 3 equal volumes of 30mL which will be exposed to 100uL DMSO, 0.01mg/mL mupirocin, or 0.1mg/mL decoyinine for 15 minutes. At this point, 10mL sample will be removed for protein analysis. The remaining 20mL will be harvested by fast filtration for analysis.","TREATMENT_COMPOUND":"DMSO|Mupirocin|Decoyinine","TREATMENT_DOSE":"100uL|0.01mg/mL|0.1mg/mL","TREATMENT_DOSEDURATION":"15 min|15 min|15 min","TREATMENT_VEHICLE":"DMSO|DMSO|DMSO"},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"NAD-ATP","SAMPLEPREP_PROTOCOL_FILENAME":"SB_NAD-ATP_Assay_Agilent.pdf"},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_SUMMARY":"NAD-ATP","CHROMATOGRAPHY_TYPE":"Reversed phase","INSTRUMENT_NAME":"Agilent 1290 Infinity","COLUMN_NAME":"Thermo Hypercarb (50 x 2.1mm, 3um)","METHODS_FILENAME":"SB_NAD-ATP_Assay_Agilent.pdf"},

"ANALYSIS":{"ANALYSIS_TYPE":"MS","ANALYSIS_PROTOCOL_FILE":"SB_NAD-ATP_Assay_Agilent.pdf"},

"MS":{"MS_COMMENTS":"-","INSTRUMENT_NAME":"Agilent 6490 QQQ","INSTRUMENT_TYPE":"Triple quadrupole","MS_TYPE":"ESI","ION_MODE":"POSITIVE"},

"MS_METABOLITE_DATA":{
"Units":"nmol/mg protein",

"Data":[{"Metabolite":"NMN","OG1RF_1 DMSO":"0.05","OG1RF_2 DMSO":"0.07","OG1RF_3 DMSO":"0.08","OG1RF_1 Mup":"0.04","OG1RF_2 Mup":"N.D.","OG1RF_3 Mup":"0.07","OG1RF_1 Decoy":"0.11","OG1RF_2 Decoy":"0.08","OG1RF_3 Decoy":"0.13"},{"Metabolite":"NAD","OG1RF_1 DMSO":"2.33","OG1RF_2 DMSO":"2.72","OG1RF_3 DMSO":"2.73","OG1RF_1 Mup":"3.87","OG1RF_2 Mup":"N.D.","OG1RF_3 Mup":"4.59","OG1RF_1 Decoy":"5.54","OG1RF_2 Decoy":"5.49","OG1RF_3 Decoy":"6.31"},{"Metabolite":"NADP","OG1RF_1 DMSO":"0.25","OG1RF_2 DMSO":"0.29","OG1RF_3 DMSO":"0.31","OG1RF_1 Mup":"0.34","OG1RF_2 Mup":"N.D.","OG1RF_3 Mup":"0.40","OG1RF_1 Decoy":"0.44","OG1RF_2 Decoy":"0.42","OG1RF_3 Decoy":"0.50"},{"Metabolite":"AMP","OG1RF_1 DMSO":"1.63","OG1RF_2 DMSO":"1.48","OG1RF_3 DMSO":"1.26","OG1RF_1 Mup":"4.33","OG1RF_2 Mup":"N.D.","OG1RF_3 Mup":"3.87","OG1RF_1 Decoy":"6.29","OG1RF_2 Decoy":"3.68","OG1RF_3 Decoy":"7.80"},{"Metabolite":"ADP","OG1RF_1 DMSO":"","OG1RF_2 DMSO":"","OG1RF_3 DMSO":"","OG1RF_1 Mup":"","OG1RF_2 Mup":"N.D.","OG1RF_3 Mup":"","OG1RF_1 Decoy":"","OG1RF_2 Decoy":"5.58","OG1RF_3 Decoy":"5.53"},{"Metabolite":"ATP","OG1RF_1 DMSO":"0.58","OG1RF_2 DMSO":"1.17","OG1RF_3 DMSO":"1.54","OG1RF_1 Mup":"1.50","OG1RF_2 Mup":"N.D.","OG1RF_3 Mup":"3.07","OG1RF_1 Decoy":"1.91","OG1RF_2 Decoy":"4.49","OG1RF_3 Decoy":"1.93"},{"Metabolite":"GDP","OG1RF_1 DMSO":"0.699144904","OG1RF_2 DMSO":"0.814446652","OG1RF_3 DMSO":"0.864344745","OG1RF_1 Mup":"0.511195459","OG1RF_2 Mup":"N.D.","OG1RF_3 Mup":"0.57325359","OG1RF_1 Decoy":"0.705216686","OG1RF_2 Decoy":"0.603863247","OG1RF_3 Decoy":"0.735392147"},{"Metabolite":"GTP","OG1RF_1 DMSO":"","OG1RF_2 DMSO":"0.564649253","OG1RF_3 DMSO":"0.706891089","OG1RF_1 Mup":"","OG1RF_2 Mup":"N.D.","OG1RF_3 Mup":"0.413789023","OG1RF_1 Decoy":"","OG1RF_2 Decoy":"0.441168195","OG1RF_3 Decoy":""},{"Metabolite":"CDP","OG1RF_1 DMSO":"0.170140598","OG1RF_2 DMSO":"0.229450701","OG1RF_3 DMSO":"0.236300634","OG1RF_1 Mup":"0.564743115","OG1RF_2 Mup":"N.D.","OG1RF_3 Mup":"0.865106823","OG1RF_1 Decoy":"0.350493204","OG1RF_2 Decoy":"0.460581436","OG1RF_3 Decoy":"0.410636444"},{"Metabolite":"CTP","OG1RF_1 DMSO":"0.092262162","OG1RF_2 DMSO":"0.214914424","OG1RF_3 DMSO":"0.267655897","OG1RF_1 Mup":"0.316088971","OG1RF_2 Mup":"N.D.","OG1RF_3 Mup":"0.810274935","OG1RF_1 Decoy":"0.203505352","OG1RF_2 Decoy":"0.514360372","OG1RF_3 Decoy":"0.206382691"},{"Metabolite":"UDP","OG1RF_1 DMSO":"1.118681816","OG1RF_2 DMSO":"1.170668692","OG1RF_3 DMSO":"0.901959615","OG1RF_1 Mup":"1.388781358","OG1RF_2 Mup":"N.D.","OG1RF_3 Mup":"1.427531646","OG1RF_1 Decoy":"1.498960983","OG1RF_2 Decoy":"1.24000226","OG1RF_3 Decoy":"1.723860369"},{"Metabolite":"UTP","OG1RF_1 DMSO":"0.777514404","OG1RF_2 DMSO":"1.228959831","OG1RF_3 DMSO":"1.281240802","OG1RF_1 Mup":"1.096361577","OG1RF_2 Mup":"N.D.","OG1RF_3 Mup":"1.666613932","OG1RF_1 Decoy":"1.028269484","OG1RF_2 Decoy":"1.555148577","OG1RF_3 Decoy":"1.033884632"}],

"Metabolites":[{"Metabolite":"NMN","retention index":"1.13","quantified m/z":"335.2","PubChem ID":"14180","KEGG ID":""},{"Metabolite":"NAD","retention index":"1.80","quantified m/z":"664.2","PubChem ID":"5893","KEGG ID":""},{"Metabolite":"NADP","retention index":"1.64","quantified m/z":"744.2","PubChem ID":"5886","KEGG ID":""},{"Metabolite":"AMP","retention index":"1.51","quantified m/z":"348.1","PubChem ID":"6083","KEGG ID":""},{"Metabolite":"ADP","retention index":"1.51","quantified m/z":"428","PubChem ID":"6022","KEGG ID":""},{"Metabolite":"ATP","retention index":"1.50","quantified m/z":"508.1","PubChem ID":"5957","KEGG ID":""},{"Metabolite":"GDP","retention index":"","quantified m/z":"","PubChem ID":"","KEGG ID":""},{"Metabolite":"GTP","retention index":"","quantified m/z":"","PubChem ID":"","KEGG ID":""},{"Metabolite":"CDP","retention index":"","quantified m/z":"","PubChem ID":"","KEGG ID":""},{"Metabolite":"CTP","retention index":"","quantified m/z":"","PubChem ID":"","KEGG ID":""},{"Metabolite":"UDP","retention index":"","quantified m/z":"","PubChem ID":"","KEGG ID":""},{"Metabolite":"UTP","retention index":"","quantified m/z":"","PubChem ID":"","KEGG ID":""}]
}

}