{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST000317","ANALYSIS_ID":"AN000503","VERSION":"1","CREATED_ON":"January 15, 2016, 12:53 pm"},

"PROJECT":{"PROJECT_TITLE":"Role of medium in bacterial growth","PROJECT_SUMMARY":"Experiment to test how different growth mediums affect bacterial growth. The supernatants of 17 strains of bacteria (10 grown in one medium and 7 grown in another medium) were submitted for metabolite analysis.","INSTITUTE":"University of California, Davis","DEPARTMENT":"Genome and Biomedical Sciences Facility","LABORATORY":"WCMC Metabolomics Core","LAST_NAME":"Fiehn","FIRST_NAME":"Oliver","ADDRESS":"1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616","EMAIL":"ofiehn@ucdavis.edu","PHONE":"(530) 754-8258","FUNDING_SOURCE":"U24DK097154"},

"STUDY":{"STUDY_TITLE":"Role of medium in bacterial growth","STUDY_SUMMARY":"Experiment to test how different growth mediums affect bacterial growth. The supernatants of 17 strains of bacteria (10 grown in one medium and 7 grown in another medium) were submitted for metabolite analysis.","INSTITUTE":"University of California, Davis","DEPARTMENT":"Genome and Biomedical Sciences Facility","LABORATORY":"WCMC Metabolomics Core","LAST_NAME":"Fiehn","FIRST_NAME":"Oliver","ADDRESS":"1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616","EMAIL":"ofiehn@ucdavis.edu","PHONE":"(530) 754-8258","NUM_GROUPS":"4","TOTAL_SUBJECTS":"38"},

"SUBJECT":{"SUBJECT_TYPE":"Cells","SUBJECT_SPECIES":"Bacteria"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"-",
"Sample ID":"SA001",
"Factors":{"Media type":"E"},
"Additional sample data":{"Label":"E1"}
},
{
"Subject ID":"-",
"Sample ID":"SA002",
"Factors":{"Media type":"E"},
"Additional sample data":{"Label":"E2"}
},
{
"Subject ID":"-",
"Sample ID":"SA003",
"Factors":{"Media type":"E"},
"Additional sample data":{"Label":"E3"}
},
{
"Subject ID":"-",
"Sample ID":"SA004",
"Factors":{"Media type":"E"},
"Additional sample data":{"Label":"E4"}
},
{
"Subject ID":"-",
"Sample ID":"SA005",
"Factors":{"Media type":"E"},
"Additional sample data":{"Label":"E5"}
},
{
"Subject ID":"-",
"Sample ID":"SA006",
"Factors":{"Media type":"E"},
"Additional sample data":{"Label":"E6"}
},
{
"Subject ID":"-",
"Sample ID":"SA007",
"Factors":{"Media type":"E"},
"Additional sample data":{"Label":"E7"}
},
{
"Subject ID":"-",
"Sample ID":"SA008",
"Factors":{"Media type":"E"},
"Additional sample data":{"Label":"E8"}
},
{
"Subject ID":"-",
"Sample ID":"SA009",
"Factors":{"Media type":"E"},
"Additional sample data":{"Label":"E9"}
},
{
"Subject ID":"-",
"Sample ID":"SA010",
"Factors":{"Media type":"E"},
"Additional sample data":{"Label":"E10"}
},
{
"Subject ID":"-",
"Sample ID":"SA011",
"Factors":{"Media type":"E"},
"Additional sample data":{"Label":"E11"}
},
{
"Subject ID":"-",
"Sample ID":"SA012",
"Factors":{"Media type":"A"},
"Additional sample data":{"Label":"A1"}
},
{
"Subject ID":"-",
"Sample ID":"SA013",
"Factors":{"Media type":"A"},
"Additional sample data":{"Label":"A2"}
},
{
"Subject ID":"-",
"Sample ID":"SA014",
"Factors":{"Media type":"A"},
"Additional sample data":{"Label":"A3"}
},
{
"Subject ID":"-",
"Sample ID":"SA015",
"Factors":{"Media type":"A"},
"Additional sample data":{"Label":"A4"}
},
{
"Subject ID":"-",
"Sample ID":"SA016",
"Factors":{"Media type":"A"},
"Additional sample data":{"Label":"A5"}
},
{
"Subject ID":"-",
"Sample ID":"SA017",
"Factors":{"Media type":"A"},
"Additional sample data":{"Label":"A6"}
},
{
"Subject ID":"-",
"Sample ID":"SA018",
"Factors":{"Media type":"A"},
"Additional sample data":{"Label":"A7"}
},
{
"Subject ID":"-",
"Sample ID":"SA019",
"Factors":{"Media type":"A"},
"Additional sample data":{"Label":"A8"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"-","SAMPLE_TYPE":"Spent culture supernatant"},

"TREATMENT":{"TREATMENT_SUMMARY":"There are 2 treatments. Each sample is a supernatant from a different bacterial strain grown in culture.There are a total of 17 strains, 10 of which are grown in one type of medium and 7 are grown in another type of medium. Supernatants from the 2 types of media are also submitted for analysis.","TREATMENT_PROTOCOL_FILENAME":"StudyDesign_NadirMahmood_072914.pdf"},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"1. After quenching the cells add 1 X 106 dried cells to 1.5 ml eppendorff tube. 2. Place the eppendorf tube with cells on dry ice for 20 minutes or til the cells are completely frozen and ice for 20 minutes, till they are completely thawed. Repeat this step twice. 3. Add 1ml of extraction solvent which has been pre-chilled using the ThermoElectron Neslab RTE 740 cooling bath set to -20°C. to the ependorff tube with cells. 4. Repeat step 2 twice with the extraction solvent. 5. Vortex the sample for 10s and shake for 5min at 4°C using the Orbital Mixing Chilling/Heating plate. Centrifuge samples for 2min at 14000 rcf using the centrifuge Eppendorf 5415 D. 6. Aliquot two 500µL portions of the supernatant. One for analysis and one for backup. Store one aliquot in the -20°C freezer as a backup. 7. Evaporate one 500µL aliquot of the sample in the Labconco Centrivap cold trap concentrator to complete dryness. 8. Submit to derivatization.","SAMPLEPREP_PROTOCOL_FILENAME":"SOP_Extraction_of_Cell_pellets.pdf"},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_SUMMARY":"UPLC","CHROMATOGRAPHY_TYPE":"Reversed phase","INSTRUMENT_NAME":"Unspecified","COLUMN_NAME":"Waters Acquity CSH C18 (100 x 2.1mm, 1.7um) 1.7um Pre-Column","FLOW_GRADIENT":"15% B to 99% B","FLOW_RATE":"0.6 mL/min","COLUMN_TEMPERATURE":"65 C","METHODS_FILENAME":"Data Dictionary Fiehn laboratory_CSH QTOF lipidomics_05-29-2014.pdf","SOLVENT_A":"60:40 Acetonitrile:Water +10mM Ammonium Formate +10mM Formic Acid","SOLVENT_B":"9:1 Isopropanol:Acetonitrile +10mM Ammonium Formate +10mM Formic Acid","COLUMN_PRESSURE":"450-850 bar","INTERNAL_STANDARD":"See data dictionary","RETENTION_TIME":"See data dictionary","SAMPLE_INJECTION":"1.67 uL","ANALYTICAL_TIME":"13 min","CAPILLARY_VOLTAGE":"3500","TIME_PROGRAM":"15 min","WEAK_WASH_SOLVENT_NAME":"Isopropanol","WEAK_WASH_VOLUME":"5 seconds","STRONG_WASH_SOLVENT_NAME":"Isopropanol","TARGET_SAMPLE_TEMPERATURE":"Autosampler temp 4 C","RANDOMIZATION_ORDER":"Excel"},

"ANALYSIS":{"ANALYSIS_TYPE":"MS","SOFTWARE_VERSION":"MassHunter","DATA_FORMAT":".d"},

"MS":{"MS_COMMENTS":"-","INSTRUMENT_NAME":"Agilent 6530 QTOF","INSTRUMENT_TYPE":"QTOF","MS_TYPE":"ESI","ION_MODE":"POSITIVE","CAPILLARY_VOLTAGE":"3500","COLLISION_GAS":"Nitrogen","DRY_GAS_FLOW":"8 l/min","DRY_GAS_TEMP":"325","FRAGMENT_VOLTAGE":"120","FRAGMENTATION_METHOD":"Auto MS/MS","ION_SOURCE_TEMPERATURE":"325","ION_SPRAY_VOLTAGE":"1000","IONIZATION":"Pos","PRECURSOR_TYPE":"Intact Molecule","REAGENT_GAS":"Nitrogen","SOURCE_TEMPERATURE":"325 C","DESOLVATION_GAS_FLOW":"11 l/min","DESOLVATION_TEMPERATURE":"350 C","NEBULIZER":"35 psig","OCTPOLE_VOLTAGE":"750","RESOLUTION_SETTING":"Extended Dynamic Range","SCAN_RANGE_MOVERZ":"60-1700 Da","SCANNING_CYCLE":"2 Hz","SCANNING_RANGE":"60-1700 Da","SKIMMER_VOLTAGE":"65"},

"MS_METABOLITE_DATA":{
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