{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST000469","ANALYSIS_ID":"AN000733","VERSION":"1","CREATED_ON":"September 12, 2016, 3:23 pm"},

"PROJECT":{"PROJECT_TITLE":"Enterococcus faecalis nucleotie profiles","PROJECT_SUMMARY":"Determination of metabolite profiles of E. faecalis strains OG1RF (WT) and rel/relQ (ppGpp0)","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 - pilot","STUDY_TYPE":"Comparison between wild-type and mutant strain, as well as providing varying cell count input for WT","STUDY_SUMMARY":"E. faecalis OG1RF and rel/relQ will be grown in FMC-AUG to OD600 = 0.25. 3E10 cells will be harvested by fast filtration, scraped off of membrane into ice-cold PBS, and pelleted by centrifugation. This process will be repeated with OG1RF only to harvest 3E9 and 3E8 cells. A second OG1RF sample of 3E10 cells will be scraped into formic acid; only acid-soluble extract willl be sent for this sample.","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":"5","TOTAL_SUBJECTS":"5"},

"SUBJECT":{"SUBJECT_TYPE":"Bacterial cells","SUBJECT_SPECIES":"Enterococcus faecalis","TAXONOMY_ID":"1351","GENOTYPE_STRAIN":"OG1RF"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"Lemos_001",
"Sample ID":"OG1RF_3E10",
"Factors":{"Strain":"WT","Resuspension":"PBS"},
"Additional sample data":{"CFU":"3.00E+10"}
},
{
"Subject ID":"Lemos_002",
"Sample ID":"OG1RF_3E9",
"Factors":{"Strain":"WT","Resuspension":"PBS"},
"Additional sample data":{"CFU":"3.00E+09"}
},
{
"Subject ID":"Lemos_003",
"Sample ID":"OG1RF_3E8",
"Factors":{"Strain":"WT","Resuspension":"PBS"},
"Additional sample data":{"CFU":"3.00E+08"}
},
{
"Subject ID":"Lemos_004",
"Sample ID":"rel/relQ_3E10",
"Factors":{"Strain":"(p)ppGpp0","Resuspension":"PBS"},
"Additional sample data":{"CFU":"3.00E+10"}
},
{
"Subject ID":"Lemos_005",
"Sample ID":"OG1RF_3E10_acid",
"Factors":{"Strain":"WT","Resuspension":"1M Formic Acid"},
"Additional sample data":{"CFU":"3.00E+10"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"3E9, 3E10 - upon reaching OD600 = 0.25, 100mL (OG1RF) or 425mL (rel/relQ) will be harvested by filtration onto 0.45uM nitrocellulose membrane. The cells will be scraped off of the membrane into ice-cold PBS or formic acid (~1 mL), centrifuged for 45 seconds at 12K RPM, liquid aspirated and stored at -80C until sending for analysis.|3E8 - (OG1RF only). Upon reaching OD600 = 0.25, 1mL culture will be harvested by 45 seconds centrifugation at 12K RPM, liquid decanted, and stored at -80C until sending for analysis.","SAMPLE_TYPE":"Bacterial cells"},

"TREATMENT":{"TREATMENT_SUMMARY":"This pilot study involves no treatment - cells will be grown in chemically defined medium to an OD600 of 0.25 and harvested for analysis"},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"NAD|NADH","SAMPLEPREP_PROTOCOL_FILENAME":"SB_NAD-ATP_Assay_Agilent.pdf;SB_NADH_Assay_Agilent.pdf"},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_SUMMARY":"NADH","CHROMATOGRAPHY_TYPE":"Reversed phase","INSTRUMENT_NAME":"Agilent 1290 Infinity","COLUMN_NAME":"Waters Acquity HSS T3 (100 x 2.1mm, 1.8um)","METHODS_FILENAME":"SB_NADH_Assay_Agilent.pdf"},

"ANALYSIS":{"ANALYSIS_TYPE":"MS"},

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

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

"Data":[{"Metabolite":"AMP","OG1RF_3E10":"0.845457492","OG1RF_3E9":"","OG1RF_3E8":"","rel/relQ_3E10":"0.255958742","OG1RF_3E10_acid":"0.377771343"},{"Metabolite":"ADP","OG1RF_3E10":"2.377354704","OG1RF_3E9":"2.260149639","OG1RF_3E8":"5.589016127","rel/relQ_3E10":"1.694243851","OG1RF_3E10_acid":"3.516579009"},{"Metabolite":"ATP","OG1RF_3E10":"4.654067744","OG1RF_3E9":"5.208946868","OG1RF_3E8":"","rel/relQ_3E10":"6.989888429","OG1RF_3E10_acid":"1.025161287"},{"Metabolite":"GDP","OG1RF_3E10":"0.760383757","OG1RF_3E9":"0.739643642","OG1RF_3E8":"","rel/relQ_3E10":"0.419042181","OG1RF_3E10_acid":"0.562394336"},{"Metabolite":"GTP","OG1RF_3E10":"1.286746555","OG1RF_3E9":"1.413418092","OG1RF_3E8":"","rel/relQ_3E10":"2.632834242","OG1RF_3E10_acid":"0.218756027"},{"Metabolite":"CDP","OG1RF_3E10":"0.382224859","OG1RF_3E9":"0.31849744","OG1RF_3E8":"","rel/relQ_3E10":"0.411867","OG1RF_3E10_acid":"0.655777432"},{"Metabolite":"CTP","OG1RF_3E10":"0.988035124","OG1RF_3E9":"1.219911451","OG1RF_3E8":"1.078961586","rel/relQ_3E10":"2.477695127","OG1RF_3E10_acid":"0.323393839"},{"Metabolite":"UDP","OG1RF_3E10":"0.87831059","OG1RF_3E9":"0.779262793","OG1RF_3E8":"1.349374202","rel/relQ_3E10":"0.590703813","OG1RF_3E10_acid":"1.10056381"},{"Metabolite":"UTP","OG1RF_3E10":"3.223402275","OG1RF_3E9":"3.796559869","OG1RF_3E8":"3.217282727","rel/relQ_3E10":"4.902149993","OG1RF_3E10_acid":"0.763308277"}],

"Metabolites":[{"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":"1.5","quantified m/z":"508.1","PubChem ID":"5957","KEGG ID":""},{"Metabolite":"GDP","retention index":"2.71","quantified m/z":"444.1","PubChem ID":"8977","KEGG ID":""},{"Metabolite":"GTP","retention index":"2.78","quantified m/z":"524","PubChem ID":"6830","KEGG ID":""},{"Metabolite":"CDP","retention index":"1.65","quantified m/z":"404.1","PubChem ID":"6132","KEGG ID":""},{"Metabolite":"CTP","retention index":"1.67","quantified m/z":"484","PubChem ID":"6176","KEGG ID":""},{"Metabolite":"UDP","retention index":"1.72","quantified m/z":"405","PubChem ID":"6031","KEGG ID":""},{"Metabolite":"UTP","retention index":"1.79","quantified m/z":"485","PubChem ID":"6133","KEGG ID":""}]
}

}