{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST000340","ANALYSIS_ID":"AN000552","VERSION":"1","CREATED_ON":"January 22, 2016, 3:46 pm"},

"PROJECT":{"PROJECT_TITLE":"Metformin effects on liver and kidney tissue","PROJECT_SUMMARY":"This experiment aimed to discover the effects of metformin on mouse liver and kidney tissue. The effects were seen by comparing the liver of the metformin group to the liver of a control group of mice treated given saline solution.","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":"NIH U24DK097154"},

"STUDY":{"STUDY_TITLE":"Metformin effects on liver and kidney tissue","STUDY_SUMMARY":"This experiment aimed to discover the effects of metformin on mouse liver and kidney tissue. The effects were seen by comparing the liver of the metformin group to the liver of a control group of mice treated given saline solution.","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":"20"},

"SUBJECT":{"SUBJECT_TYPE":"Mus musculus","SUBJECT_SPECIES":"Mus musculus","TAXONOMY_ID":"10090"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"Kidney_MET IP 7day mouse-1",
"Sample ID":"Inj04_Kid Met_1",
"Factors":{"Treatment":"Metformin","Organ":"Kidney"},
"Additional sample data":{"Species":"Mus Musculus"}
},
{
"Subject ID":"Kidney_MET IP 7day mouse-2",
"Sample ID":"Inj07_Kid Met_2",
"Factors":{"Treatment":"Metformin","Organ":"Kidney"},
"Additional sample data":{"Species":"Mus Musculus"}
},
{
"Subject ID":"Kidney_MET IP 7day mouse-3",
"Sample ID":"Inj09_Kid Met_3",
"Factors":{"Treatment":"Metformin","Organ":"Kidney"},
"Additional sample data":{"Species":"Mus Musculus"}
},
{
"Subject ID":"Kidney_MET IP 7day mouse-4",
"Sample ID":"Inj19_Kid Met_4",
"Factors":{"Treatment":"Metformin","Organ":"Kidney"},
"Additional sample data":{"Species":"Mus Musculus"}
},
{
"Subject ID":"Kidney_MET IP 7day mouse-5",
"Sample ID":"Inj02_Kid Met_5",
"Factors":{"Treatment":"Metformin","Organ":"Kidney"},
"Additional sample data":{"Species":"Mus Musculus"}
},
{
"Subject ID":"Kidney_Saline 7day mouse-1",
"Sample ID":"Inj01_Kid Sal_1",
"Factors":{"Treatment":"Saline","Organ":"Kidney"},
"Additional sample data":{"Species":"Mus Musculus"}
},
{
"Subject ID":"Kidney_Saline 7day mouse-2",
"Sample ID":"Inj12_Kid Sal_2",
"Factors":{"Treatment":"Saline","Organ":"Kidney"},
"Additional sample data":{"Species":"Mus Musculus"}
},
{
"Subject ID":"Kidney_Saline 7day mouse-3",
"Sample ID":"Inj17_Kid Sal_3",
"Factors":{"Treatment":"Saline","Organ":"Kidney"},
"Additional sample data":{"Species":"Mus Musculus"}
},
{
"Subject ID":"Kidney_Saline 7day mouse-4",
"Sample ID":"Inj15_Kid Sal_4",
"Factors":{"Treatment":"Saline","Organ":"Kidney"},
"Additional sample data":{"Species":"Mus Musculus"}
},
{
"Subject ID":"Kidney_Saline 7day mouse-5",
"Sample ID":"Inj03_Kid Sal_5",
"Factors":{"Treatment":"Saline","Organ":"Kidney"},
"Additional sample data":{"Species":"Mus Musculus"}
},
{
"Subject ID":"Liver_MET IP 7day mouse-1",
"Sample ID":"Inj18_Liv Met_1",
"Factors":{"Treatment":"Metformin","Organ":"Liver"},
"Additional sample data":{"Species":"Mus Musculus"}
},
{
"Subject ID":"Liver_MET IP 7day mouse-2",
"Sample ID":"Inj06_Liv Met_2",
"Factors":{"Treatment":"Metformin","Organ":"Liver"},
"Additional sample data":{"Species":"Mus Musculus"}
},
{
"Subject ID":"Liver_MET IP 7day mouse-3",
"Sample ID":"Inj13_Liv Met_3",
"Factors":{"Treatment":"Metformin","Organ":"Liver"},
"Additional sample data":{"Species":"Mus Musculus"}
},
{
"Subject ID":"Liver_MET IP 7day mouse-4",
"Sample ID":"Inj20_Liv Met_4",
"Factors":{"Treatment":"Metformin","Organ":"Liver"},
"Additional sample data":{"Species":"Mus Musculus"}
},
{
"Subject ID":"Liver_MET IP 7day mouse-5",
"Sample ID":"Inj11_Liv Met_5",
"Factors":{"Treatment":"Metformin","Organ":"Liver"},
"Additional sample data":{"Species":"Mus Musculus"}
},
{
"Subject ID":"Liver_Saline 7day mouse-1",
"Sample ID":"Inj10_Liv Sal_1",
"Factors":{"Treatment":"Saline","Organ":"Liver"},
"Additional sample data":{"Species":"Mus Musculus"}
},
{
"Subject ID":"Liver_Saline 7day mouse-2",
"Sample ID":"Inj16_Liv Sal_2",
"Factors":{"Treatment":"Saline","Organ":"Liver"},
"Additional sample data":{"Species":"Mus Musculus"}
},
{
"Subject ID":"Liver_Saline 7day mouse-3",
"Sample ID":"Inj05_Liv Sal_3",
"Factors":{"Treatment":"Saline","Organ":"Liver"},
"Additional sample data":{"Species":"Mus Musculus"}
},
{
"Subject ID":"Liver_Saline 7day mouse-4",
"Sample ID":"Inj08_Liv Sal_4",
"Factors":{"Treatment":"Saline","Organ":"Liver"},
"Additional sample data":{"Species":"Mus Musculus"}
},
{
"Subject ID":"Liver_Saline 7day mouse-5",
"Sample ID":"Inj14_Liv Sal_5",
"Factors":{"Treatment":"Saline","Organ":"Liver"},
"Additional sample data":{"Species":"Mus Musculus"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"Liver tissues were isolated and frozen down in liquid nitrogen.","COLLECTION_PROTOCOL_FILENAME":"SookWahYee_StudyDesign_5.13.14.pdf","SAMPLE_TYPE":"Liver and Kidney tissue"},

"TREATMENT":{"TREATMENT_SUMMARY":"5 mice were treated with biguanide (metformin) and 5 mice were treated with saline. Liver tissues were obtained 7 days after treatment.","TREATMENT_PROTOCOL_FILENAME":"SookWahYee_StudyDesign_5.13.14.pdf"},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"1. Weigh 4mg tissue sample in to a 2mL Eppendorf tube. 2. Add 1mL extraction solvent to the tissue sample and homogenize for 45 seconds ensuring that sample resembles a powder. In between samples, clean the homogenizer in solutions of methanol, acetone, water, and the extraction solvent in the order listed. 3. Vortex samples for 10 seconds, then 5 minutes on 4°C shaker. 4. Centrifuge the samples for 2 minutes at 14,000 rcf. Aliquot 500μL supernatant for analysis, and 500μL for a backup. Store backup aliquots in the -20°C freezer. 5. Evaporate one 500μl analysis aliquot in the Labconco Centrivap cold trap concentrator to complete dryness (typically overnight). 6. The dried aliquot is then re-suspended with 500l 50% acetonitrile (degassed as given) 7. Centrifuge for 2 minutes at 14,000 rcf using the centrifuge Eppendorf 5415. 8. Remove supernatant to a new Eppendorf tube. 9. Evaporate the supernatant to dryness in the the Labconco Centrivap cold trap concentrator. 10. Submit to derivatization.","SAMPLEPREP_PROTOCOL_FILENAME":"SOP Extraction of Liver Tissue Samples.pdf"},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_TYPE":"None","INSTRUMENT_NAME":"Unspecified","COLUMN_NAME":"Waters Acquity BEH Amide (150 x 2.1mm, 1.7um) Waters Acquity UPLC BEH Amide VanGuard pre-column (1.7 μm , 5 mm × 2.1 mm;)","FLOW_GRADIENT":"100% B to 30% B","FLOW_RATE":"0.4 mL/min","COLUMN_TEMPERATURE":"45 C","METHODS_FILENAME":"Data Dictionary Fiehn laboratory_HILIC QTOF MS.pdf","COLUMN_PRESSURE":"200-700 bar","INJECTION_TEMPERATURE":"4 C","INTERNAL_STANDARD":"See data dictionary","SAMPLE_INJECTION":"3 μL","ANALYTICAL_TIME":"14 min","CAPILLARY_VOLTAGE":"4500","TIME_PROGRAM":"16.75 min","WEAK_WASH_SOLVENT_NAME":"1:1 ACN:H2O","WEAK_WASH_VOLUME":"5 seconds","TARGET_SAMPLE_TEMPERATURE":"Autosampler temp 4 C","RANDOMIZATION_ORDER":"Excel"},

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

"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","DATAFORMAT":".d","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":{
"Units":"Peak height",

"Data":[{"Metabolite":"2-Aminobenzoic acid","Inj04_Kid Met_1":"234805","Inj07_Kid Met_2":"307789","Inj09_Kid Met_3":"302382","Inj19_Kid Met_4":"239810","Inj02_Kid Met_5":"177267","Inj01_Kid Sal_1":"206130","Inj12_Kid Sal_2":"215351","Inj17_Kid Sal_3":"115704","Inj15_Kid Sal_4":"215865","Inj03_Kid Sal_5":"227503","Inj18_Liv Met_1":"214790","Inj06_Liv Met_2":"235019","Inj13_Liv Met_3":"192091","Inj20_Liv Met_4":"243019","Inj11_Liv Met_5":"110489","Inj10_Liv Sal_1":"114865","Inj16_Liv Sal_2":"208407","Inj05_Liv Sal_3":"92622","Inj08_Liv Sal_4":"105065","Inj14_Liv Sal_5":"223748"},{"Metabolite":"Acylcarnitine (C2:0)","Inj04_Kid Met_1":"2256979","Inj07_Kid Met_2":"5689386","Inj09_Kid Met_3":"6128560","Inj19_Kid Met_4":"6142862","Inj02_Kid Met_5":"2963201","Inj01_Kid Sal_1":"3057598","Inj12_Kid Sal_2":"2257984","Inj17_Kid Sal_3":"1843135","Inj15_Kid Sal_4":"4965413","Inj03_Kid Sal_5":"4190516","Inj18_Liv Met_1":"91186","Inj06_Liv Met_2":"40176","Inj13_Liv Met_3":"76505","Inj20_Liv Met_4":"58760","Inj11_Liv Met_5":"46488","Inj10_Liv Sal_1":"79301","Inj16_Liv Sal_2":"214671","Inj05_Liv Sal_3":"212636","Inj08_Liv Sal_4":"99855","Inj14_Liv Sal_5":"203705"},{"Metabolite":"Acylcarnitine (C3:0)","Inj04_Kid Met_1":"1861374","Inj07_Kid Met_2":"1464259","Inj09_Kid Met_3":"1208306","Inj19_Kid Met_4":"1149839","Inj02_Kid Met_5":"1073042","Inj01_Kid Sal_1":"310450","Inj12_Kid Sal_2":"282886","Inj17_Kid Sal_3":"189193","Inj15_Kid Sal_4":"1462412","Inj03_Kid Sal_5":"1726932","Inj18_Liv Met_1":"224925","Inj06_Liv Met_2":"65158","Inj13_Liv Met_3":"122185","Inj20_Liv Met_4":"76878","Inj11_Liv Met_5":"39191","Inj10_Liv Sal_1":"143177","Inj16_Liv Sal_2":"236758","Inj05_Liv Sal_3":"448984","Inj08_Liv Sal_4":"98188","Inj14_Liv Sal_5":"160975"},{"Metabolite":"Acylcarnitine (C4:0)","Inj04_Kid Met_1":"95599","Inj07_Kid Met_2":"57920","Inj09_Kid Met_3":"42193","Inj19_Kid Met_4":"144810","Inj02_Kid Met_5":"53872","Inj01_Kid Sal_1":"66810","Inj12_Kid Sal_2":"94730","Inj17_Kid Sal_3":"50247","Inj15_Kid Sal_4":"36010","Inj03_Kid Sal_5":"107863","Inj18_Liv Met_1":"26117","Inj06_Liv Met_2":"13532","Inj13_Liv Met_3":"14547","Inj20_Liv Met_4":"11940","Inj11_Liv Met_5":"12359","Inj10_Liv Sal_1":"20571","Inj16_Liv Sal_2":"25348","Inj05_Liv Sal_3":"26948","Inj08_Liv Sal_4":"12544","Inj14_Liv Sal_5":"39842"},{"Metabolite":"Arginine","Inj04_Kid Met_1":"296549","Inj07_Kid Met_2":"348304","Inj09_Kid Met_3":"369495","Inj19_Kid Met_4":"389957","Inj02_Kid Met_5":"539775","Inj01_Kid Sal_1":"484067","Inj12_Kid Sal_2":"449902","Inj17_Kid Sal_3":"200642","Inj15_Kid Sal_4":"372706","Inj03_Kid Sal_5":"438399","Inj18_Liv Met_1":"4529","Inj06_Liv Met_2":"4931","Inj13_Liv Met_3":"6296","Inj20_Liv Met_4":"5832","Inj11_Liv Met_5":"4128","Inj10_Liv Sal_1":"8080","Inj16_Liv Sal_2":"5384","Inj05_Liv Sal_3":"7177","Inj08_Liv Sal_4":"5663","Inj14_Liv Sal_5":"4819"},{"Metabolite":"Creatine","Inj04_Kid Met_1":"2723559","Inj07_Kid Met_2":"2348455","Inj09_Kid Met_3":"2227557","Inj19_Kid Met_4":"2292174","Inj02_Kid Met_5":"2575708","Inj01_Kid Sal_1":"2209961","Inj12_Kid Sal_2":"2446914","Inj17_Kid Sal_3":"1991563","Inj15_Kid Sal_4":"2253373","Inj03_Kid Sal_5":"2769658","Inj18_Liv Met_1":"1747526","Inj06_Liv Met_2":"1310417","Inj13_Liv Met_3":"1239875","Inj20_Liv Met_4":"1404825","Inj11_Liv Met_5":"1124783","Inj10_Liv Sal_1":"1180325","Inj16_Liv Sal_2":"1491500","Inj05_Liv Sal_3":"1375101","Inj08_Liv Sal_4":"1034059","Inj14_Liv Sal_5":"1427944"},{"Metabolite":"gamma-Butyrobetaine","Inj04_Kid Met_1":"56426","Inj07_Kid Met_2":"54662","Inj09_Kid Met_3":"45840","Inj19_Kid Met_4":"65119","Inj02_Kid Met_5":"34148","Inj01_Kid Sal_1":"47076","Inj12_Kid Sal_2":"37520","Inj17_Kid Sal_3":"32818","Inj15_Kid Sal_4":"40585","Inj03_Kid Sal_5":"37787","Inj18_Liv Met_1":"37014","Inj06_Liv Met_2":"38563","Inj13_Liv Met_3":"35237","Inj20_Liv Met_4":"26818","Inj11_Liv Met_5":"26279","Inj10_Liv Sal_1":"22267","Inj16_Liv Sal_2":"25795","Inj05_Liv Sal_3":"23610","Inj08_Liv Sal_4":"23715","Inj14_Liv Sal_5":"23531"},{"Metabolite":"Glutamic acid","Inj04_Kid Met_1":"959948","Inj07_Kid Met_2":"1202142","Inj09_Kid Met_3":"1127508","Inj19_Kid Met_4":"1019410","Inj02_Kid Met_5":"1185431","Inj01_Kid Sal_1":"1120746","Inj12_Kid Sal_2":"1209036","Inj17_Kid Sal_3":"721225","Inj15_Kid Sal_4":"1378184","Inj03_Kid Sal_5":"1253484","Inj18_Liv Met_1":"335944","Inj06_Liv Met_2":"175283","Inj13_Liv Met_3":"111940","Inj20_Liv Met_4":"230674","Inj11_Liv Met_5":"149092","Inj10_Liv Sal_1":"160055","Inj16_Liv Sal_2":"156421","Inj05_Liv Sal_3":"167054","Inj08_Liv Sal_4":"156556","Inj14_Liv Sal_5":"177385"},{"Metabolite":"Hypoxanthine","Inj04_Kid Met_1":"1774943","Inj07_Kid Met_2":"1592810","Inj09_Kid Met_3":"1523331","Inj19_Kid Met_4":"1723034","Inj02_Kid Met_5":"1887206","Inj01_Kid Sal_1":"2147330","Inj12_Kid Sal_2":"2307587","Inj17_Kid Sal_3":"1263009","Inj15_Kid Sal_4":"1508313","Inj03_Kid Sal_5":"2222660","Inj18_Liv Met_1":"896939","Inj06_Liv Met_2":"556519","Inj13_Liv Met_3":"543375","Inj20_Liv Met_4":"633953","Inj11_Liv Met_5":"497578","Inj10_Liv Sal_1":"481882","Inj16_Liv Sal_2":"510631","Inj05_Liv Sal_3":"461200","Inj08_Liv Sal_4":"460379","Inj14_Liv Sal_5":"615663"},{"Metabolite":"LPC(16:1)","Inj04_Kid Met_1":"28486","Inj07_Kid Met_2":"23802","Inj09_Kid Met_3":"26084","Inj19_Kid Met_4":"28103","Inj02_Kid Met_5":"32450","Inj01_Kid Sal_1":"48697","Inj12_Kid Sal_2":"39924","Inj17_Kid Sal_3":"35201","Inj15_Kid Sal_4":"47163","Inj03_Kid Sal_5":"36149","Inj18_Liv Met_1":"329026","Inj06_Liv Met_2":"149622","Inj13_Liv Met_3":"163856","Inj20_Liv Met_4":"233469","Inj11_Liv Met_5":"154373","Inj10_Liv Sal_1":"299679","Inj16_Liv Sal_2":"228312","Inj05_Liv Sal_3":"283229","Inj08_Liv Sal_4":"190205","Inj14_Liv Sal_5":"312060"},{"Metabolite":"LPC(20:3)","Inj04_Kid Met_1":"35543","Inj07_Kid Met_2":"100111","Inj09_Kid Met_3":"88064","Inj19_Kid Met_4":"103064","Inj02_Kid Met_5":"110646","Inj01_Kid Sal_1":"43902","Inj12_Kid Sal_2":"95900","Inj17_Kid Sal_3":"78117","Inj15_Kid Sal_4":"110811","Inj03_Kid Sal_5":"58877","Inj18_Liv Met_1":"290172","Inj06_Liv Met_2":"215057","Inj13_Liv Met_3":"283385","Inj20_Liv Met_4":"311576","Inj11_Liv Met_5":"268034","Inj10_Liv Sal_1":"336896","Inj16_Liv Sal_2":"209351","Inj05_Liv Sal_3":"239021","Inj08_Liv Sal_4":"146621","Inj14_Liv Sal_5":"219442"},{"Metabolite":"LPC(20:4)","Inj04_Kid Met_1":"403128","Inj07_Kid Met_2":"342086","Inj09_Kid Met_3":"260879","Inj19_Kid Met_4":"375974","Inj02_Kid Met_5":"448417","Inj01_Kid Sal_1":"463660","Inj12_Kid Sal_2":"406621","Inj17_Kid Sal_3":"297591","Inj15_Kid Sal_4":"423715","Inj03_Kid Sal_5":"595284","Inj18_Liv Met_1":"1539297","Inj06_Liv Met_2":"1009483","Inj13_Liv Met_3":"1130553","Inj20_Liv Met_4":"1424419","Inj11_Liv Met_5":"1240347","Inj10_Liv Sal_1":"1345394","Inj16_Liv Sal_2":"991306","Inj05_Liv Sal_3":"1028235","Inj08_Liv Sal_4":"651354","Inj14_Liv Sal_5":"1140261"},{"Metabolite":"LPC(22:5)","Inj04_Kid Met_1":"89071","Inj07_Kid Met_2":"81161","Inj09_Kid Met_3":"80759","Inj19_Kid Met_4":"70525","Inj02_Kid Met_5":"116578","Inj01_Kid Sal_1":"33466","Inj12_Kid Sal_2":"82627","Inj17_Kid Sal_3":"54884","Inj15_Kid Sal_4":"110592","Inj03_Kid Sal_5":"162370","Inj18_Liv Met_1":"144472","Inj06_Liv Met_2":"145975","Inj13_Liv Met_3":"164713","Inj20_Liv Met_4":"207126","Inj11_Liv Met_5":"171241","Inj10_Liv Sal_1":"183318","Inj16_Liv Sal_2":"129110","Inj05_Liv Sal_3":"54781","Inj08_Liv Sal_4":"80566","Inj14_Liv Sal_5":"58994"},{"Metabolite":"LPC(22:6)","Inj04_Kid Met_1":"951583","Inj07_Kid Met_2":"915444","Inj09_Kid Met_3":"924621","Inj19_Kid Met_4":"747718","Inj02_Kid Met_5":"1297363","Inj01_Kid Sal_1":"993298","Inj12_Kid Sal_2":"939630","Inj17_Kid Sal_3":"645222","Inj15_Kid Sal_4":"1223360","Inj03_Kid Sal_5":"1743861","Inj18_Liv Met_1":"1632929","Inj06_Liv Met_2":"1656482","Inj13_Liv Met_3":"1745436","Inj20_Liv Met_4":"2061253","Inj11_Liv Met_5":"1888318","Inj10_Liv Sal_1":"1978820","Inj16_Liv Sal_2":"1444271","Inj05_Liv 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