{ "METABOLOMICS WORKBENCH":{"STUDY_ID":"ST000117","ANALYSIS_ID":"AN000198","VERSION":"1","CREATED_ON":"2016-09-17"}, "PROJECT":{"PROJECT_TITLE":"Metabolomics analysis of multiple metabolic functions in the YjgF/YER057c/UK114 protein family","PROJECT_SUMMARY":"-","INSTITUTE":"University of California, Davis","DEPARTMENT":"Genome Center","LABORATORY":"Fiehn Laboratory","LAST_NAME":"Fiehn","FIRST_NAME":"Oliver","ADDRESS":"451 Health Sciences Drive, Davis, California 95616, USA","EMAIL":"ofiehn@ucdavis.edu","PHONE":"-","FUNDING_SOURCE":"U.S. National Science Foundation award MCB-1153413"}, "STUDY":{"STUDY_TITLE":"Metabolomics analysis of multiple metabolic functions in the YjgF/YER057c/UK114 protein family GC-MS (Part 1)","STUDY_TYPE":"wildtype vs knock-out","STUDY_SUMMARY":"Metabolomics analysis of wild-type S. enterica, single RidA knock-out and Rid (ridA Rid2 Rid7) knock-out S.enterica cells","INSTITUTE":"University of California, Davis","DEPARTMENT":"Genome Center","LABORATORY":"Fiehn Laboratory","LAST_NAME":"ElBadawi-Sidhu","FIRST_NAME":"Mona","ADDRESS":"451 Health Sciences Drive, Davis, California 95616, USA","EMAIL":"mmelbadawi@ucdavis.edu","PHONE":"-","NUM_GROUPS":"3","TOTAL_SUBJECTS":"6"}, "SUBJECT":{"SUBJECT_TYPE":"Bacterial cells","SUBJECT_SPECIES":"Salmonella enterica;Escherichia coli","GENOTYPE_STRAIN":"DM3480|DM14100|Salmonella enterica subsp.enterica serovar Typhimurium |yjeF::kan","SPECIES_GROUP":"Microorganism"}, "SUBJECT_SAMPLE_FACTORS":[ { "Subject ID":"-", "Sample ID":"140826bmssa03_1", "Factors":{"genotype":"single RidA knockout"} }, { "Subject ID":"-", "Sample ID":"140826bmssa06_1", "Factors":{"genotype":"single RidA knockout"} }, { "Subject ID":"-", "Sample ID":"140826bmssa07_1", "Factors":{"genotype":"single RidA knockout"} }, { "Subject ID":"-", "Sample ID":"140826bmssa09_1", "Factors":{"genotype":"single RidA knockout"} }, { "Subject ID":"-", "Sample ID":"140826bmssa10_1", "Factors":{"genotype":"single RidA knockout"} }, { "Subject ID":"-", "Sample ID":"140826bmssa16_1", "Factors":{"genotype":"single RidA knockout"} }, { "Subject ID":"-", "Sample ID":"140826bmssa01_1", "Factors":{"genotype":"triple RidA knockout"} }, { "Subject ID":"-", "Sample ID":"140826bmssa04_1", "Factors":{"genotype":"triple RidA knockout"} }, { "Subject ID":"-", "Sample ID":"140826bmssa05_1", "Factors":{"genotype":"triple RidA knockout"} }, { "Subject ID":"-", "Sample ID":"140826bmssa15_1", "Factors":{"genotype":"triple RidA knockout"} }, { "Subject ID":"-", "Sample ID":"140826bmssa17_1", "Factors":{"genotype":"triple RidA knockout"} }, { "Subject ID":"-", "Sample ID":"140826bmssa18_1", "Factors":{"genotype":"triple RidA knockout"} }, { "Subject ID":"-", "Sample ID":"140826bmssa02_1", "Factors":{"genotype":"Wild Type"} }, { "Subject ID":"-", "Sample ID":"140826bmssa08_1", "Factors":{"genotype":"Wild Type"} }, { "Subject ID":"-", "Sample ID":"140826bmssa11_1", "Factors":{"genotype":"Wild Type"} }, { "Subject ID":"-", "Sample ID":"140826bmssa12_1", "Factors":{"genotype":"Wild Type"} }, { "Subject ID":"-", "Sample ID":"140826bmssa13_1", "Factors":{"genotype":"Wild Type"} }, { "Subject ID":"-", "Sample ID":"140826bmssa14_1", "Factors":{"genotype":"Wild Type"} } ], "COLLECTION":{"COLLECTION_SUMMARY":"-","SAMPLE_TYPE":"Bacterial Cells","COLLECTION_METHOD":"6 independent colonies of each cell line were grown in M9 minimal medium at 37C OD600 reached 1.5-2.0. An equivalent of 1 mL at OD 2.0 was placed into a 1.5 mL tube and spun for 15 sec. After removal of a 0.5 mL medium aliquot, remaining was removed and cell pellet was frozen in liquid nitrogen.","COLLECTION_LOCATION":"University of Florida, Gainesville","COLLECTION_VIALS":"1.5 mL eppendorf tube","STORAGE_VIALS":"1.5 mL eppendorf tube"}, "TREATMENT":{"TREATMENT_SUMMARY":"-"}, "SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"-","EXTRACTION_METHOD":"1 mL of cold, degassed extraction solvent (3:3:2 acetonitrile:isopropanol:water was added to each sample, vortexed for 10 seconds, then shaken at 4C for 4 min. were spun down using a centrifuge at 14 rcf for 2 min. Aliquots (450 uL) were to 1.5 mL eppendorf tubes and dried down using a Labconco centrivap evaporator.","EXTRACT_STORAGE":"-80C","SAMPLE_DERIVATIZATION":"10 uL of 40 mg/mL methoxyamine hydrochloride in pyridine was added to room samples and shaken for 90 min at 30C. 91 uL of silyating agent (MSTFA) a set of 13 C8 - C30 fatty acid methyl ester internal standards was added and were shaken for 30 min at 37C. Derivatized samples were transferred to glass with inserts for analysis.","SAMPLE_SPIKING":"Set of 13 C8 - C30 fatty acid methyl esters (FAMES)"}, "CHROMATOGRAPHY":{"CHROMATOGRAPHY_SUMMARY":"Untargeted GC MS","CHROMATOGRAPHY_TYPE":"GC","INSTRUMENT_NAME":"Agilent 6890N","COLUMN_NAME":"Restek corporation Rtx-5Sil MS","METHODS_FILENAME":"Data_Dictionary_Fiehn_laboratory_GCTOF_MS_primary_metabolism_09-27-2013_general.pdf","COLUMN_TEMPERATURE":"50-330oC","FLOW_RATE":"1ml/min","INTERNAL_STANDARD":"fatty acid methyl esters","SAMPLE_INJECTION":"0.5uL","OVEN_TEMPERATURE":"50C for 1 min, then ramped at 20C min-1 to 330C, held constant for 5 min","TRANSFERLINE_TEMPERATURE":"280C","WASHING_BUFFER":"Ethyl Acetate","SAMPLE_LOOP_SIZE":"30 m length x 0.25 mm internal diameter","RANDOMIZATION_ORDER":"Excel generated"}, "ANALYSIS":{"ANALYSIS_TYPE":"MS","LABORATORY_NAME":"Fiehn Laboratory","ACQUISITION_DATE":"07/2014 and 08/2014","ACQUISITION_PARAMETERS_FILE":"Data_Dictionary_Fiehn_laboratory_GCTOF_MS_primary_metabolism_09-27-2013_general.pdf","SOFTWARE_VERSION":"ChromaTOF","PROCESSING_PARAMETERS_FILE":"Data_Dictionary_Fiehn_laboratory_GCTOF_MS_primary_metabolism_09-27-2013_general.pdf","DETECTOR_TYPE":"TOF","DATA_FORMAT":".peg, .txt, .cdf"}, "MS":{"INSTRUMENT_NAME":"Leco Pegasus III GC TOF","INSTRUMENT_TYPE":"GC-TOF","MS_TYPE":"EI","ION_MODE":"POSITIVE","ION_SOURCE_TEMPERATURE":"250°C","IONIZATION":"Electron Ionization (EI)","IONIZATION_ENERGY":"-70eV","MASS_ACCURACY":"Nominal","SCANNING_RANGE":"85-500 Da","MS_COMMENTS":"GCMS"}, "MS_METABOLITE_DATA":{ "Units":"Peak area", "Data":[{"Metabolite":"2_5-dihydroxypyrazine 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