{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST000962","ANALYSIS_ID":"AN001576","VERSION":"1","CREATED_ON":"April 24, 2018, 12:21 pm"},

"PROJECT":{"PROJECT_TITLE":"Metabolomics Involved in Early-Life Single Pulse Antibiotic Exposures","PROJECT_TYPE":"Timecourse treatment Vs control","PROJECT_SUMMARY":"The mice liver samples were extracted and analyzed using broad spectrum GCMS fo r the identification of compounds distinguishing the groups .","INSTITUTE":"University of North Carolina","DEPARTMENT":"NIH Eastern Regional Comprehensive Metabolomics Resource Core (UNC NRI ERCMRC)","LABORATORY":"UNC NRI ERCMRC GCMS Core","LAST_NAME":"Sumner","FIRST_NAME":"Susan","ADDRESS":"500 Laureate Way Kannapolis NC 28081","EMAIL":"susan_sumner@unc.edu","PHONE":"1-919-622-4456"},

"STUDY":{"STUDY_TITLE":"Metabolomics Involved in Early-Life Single Pulse Antibiotic Exposures - Liver (part I)","STUDY_TYPE":"Timecourse treatment Vs control","STUDY_SUMMARY":"The mice liver samples were extracted and analyzed using broad spectrum GCMS fo r the identification of compounds distinguishing the groups .","INSTITUTE":"University of North Carolina","DEPARTMENT":"NIH Eastern Regional Comprehensive Metabolomics Resource Core (UNC NRI ERCMRC)","LABORATORY":"UNC NRI ERCMRC GCMS Core","LAST_NAME":"Sumner","FIRST_NAME":"Susan","ADDRESS":"500 Laureate Way Kannapolis NC 28081","EMAIL":"susan_sumner@unc.edu","PHONE":"1-919-622-4456","NUM_GROUPS":"10","TOTAL_SUBJECTS":"86","NUM_MALES":"30","NUM_FEMALES":"56"},

"SUBJECT":{"SUBJECT_TYPE":"Mammal","SUBJECT_SPECIES":"Mus musculus","TAXONOMY_ID":"10090"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"-",
"Sample ID":"Graphical ID",
"Factors":{"Factor 1":"Group"}
},
{
"Subject ID":"-",
"Sample ID":"BL_45",
"Factors":{"Factor 1":"Control-15"}
},
{
"Subject ID":"-",
"Sample ID":"BL_46",
"Factors":{"Factor 1":"Control-15"}
},
{
"Subject ID":"-",
"Sample ID":"BL_47",
"Factors":{"Factor 1":"Control-15"}
},
{
"Subject ID":"-",
"Sample ID":"BL_48",
"Factors":{"Factor 1":"Control-15"}
},
{
"Subject ID":"-",
"Sample ID":"BL_49",
"Factors":{"Factor 1":"Control-15"}
},
{
"Subject ID":"-",
"Sample ID":"BL_50",
"Factors":{"Factor 1":"Control-15"}
},
{
"Subject ID":"-",
"Sample ID":"BL_51",
"Factors":{"Factor 1":"Control-15"}
},
{
"Subject ID":"-",
"Sample ID":"BL_52",
"Factors":{"Factor 1":"Control-15"}
},
{
"Subject ID":"-",
"Sample ID":"BL_53",
"Factors":{"Factor 1":"Control-15"}
},
{
"Subject ID":"-",
"Sample ID":"BL_54",
"Factors":{"Factor 1":"Control-15"}
},
{
"Subject ID":"-",
"Sample ID":"BL_37",
"Factors":{"Factor 1":"Control-23"}
},
{
"Subject ID":"-",
"Sample ID":"BL_38",
"Factors":{"Factor 1":"Control-23"}
},
{
"Subject ID":"-",
"Sample ID":"BL_39",
"Factors":{"Factor 1":"Control-23"}
},
{
"Subject ID":"-",
"Sample ID":"BL_40",
"Factors":{"Factor 1":"Control-23"}
},
{
"Subject ID":"-",
"Sample ID":"BL_41",
"Factors":{"Factor 1":"Control-23"}
},
{
"Subject ID":"-",
"Sample ID":"BL_42",
"Factors":{"Factor 1":"Control-23"}
},
{
"Subject ID":"-",
"Sample ID":"BL_43",
"Factors":{"Factor 1":"Control-23"}
},
{
"Subject ID":"-",
"Sample ID":"BL_44",
"Factors":{"Factor 1":"Control-23"}
},
{
"Subject ID":"-",
"Sample ID":"BL_76",
"Factors":{"Factor 1":"Control-23"}
},
{
"Subject ID":"-",
"Sample ID":"BL_77",
"Factors":{"Factor 1":"Control-23"}
},
{
"Subject ID":"-",
"Sample ID":"BL_78",
"Factors":{"Factor 1":"Control-23"}
},
{
"Subject ID":"-",
"Sample ID":"BL_79",
"Factors":{"Factor 1":"Control-23"}
},
{
"Subject ID":"-",
"Sample ID":"BL_10",
"Factors":{"Factor 1":"Control-42"}
},
{
"Subject ID":"-",
"Sample ID":"BL_17",
"Factors":{"Factor 1":"Control-42"}
},
{
"Subject ID":"-",
"Sample ID":"BL_18",
"Factors":{"Factor 1":"Control-42"}
},
{
"Subject ID":"-",
"Sample ID":"BL_19",
"Factors":{"Factor 1":"Control-42"}
},
{
"Subject ID":"-",
"Sample ID":"BL_20",
"Factors":{"Factor 1":"Control-42"}
},
{
"Subject ID":"-",
"Sample ID":"BL_21",
"Factors":{"Factor 1":"Control-42"}
},
{
"Subject ID":"-",
"Sample ID":"BL_22",
"Factors":{"Factor 1":"Control-42"}
},
{
"Subject ID":"-",
"Sample ID":"BL_23",
"Factors":{"Factor 1":"Control-42"}
},
{
"Subject ID":"-",
"Sample ID":"BL_24",
"Factors":{"Factor 1":"Control-42"}
},
{
"Subject ID":"-",
"Sample ID":"BL_7",
"Factors":{"Factor 1":"Control-42"}
},
{
"Subject ID":"-",
"Sample ID":"BL_72",
"Factors":{"Factor 1":"Control-42"}
},
{
"Subject ID":"-",
"Sample ID":"BL_73",
"Factors":{"Factor 1":"Control-42"}
},
{
"Subject ID":"-",
"Sample ID":"BL_74",
"Factors":{"Factor 1":"Control-42"}
},
{
"Subject ID":"-",
"Sample ID":"BL_75",
"Factors":{"Factor 1":"Control-42"}
},
{
"Subject ID":"-",
"Sample ID":"BL_8",
"Factors":{"Factor 1":"Control-42"}
},
{
"Subject ID":"-",
"Sample ID":"BL_80",
"Factors":{"Factor 1":"Control-42"}
},
{
"Subject ID":"-",
"Sample ID":"BL_81",
"Factors":{"Factor 1":"Control-42"}
},
{
"Subject ID":"-",
"Sample ID":"BL_68",
"Factors":{"Factor 1":"Control-70"}
},
{
"Subject ID":"-",
"Sample ID":"BL_69",
"Factors":{"Factor 1":"Control-70"}
},
{
"Subject ID":"-",
"Sample ID":"BL_70",
"Factors":{"Factor 1":"Control-70"}
},
{
"Subject ID":"-",
"Sample ID":"BL_71",
"Factors":{"Factor 1":"Control-70"}
},
{
"Subject ID":"-",
"Sample ID":"BL_27",
"Factors":{"Factor 1":"PAT15"}
},
{
"Subject ID":"-",
"Sample ID":"BL_28",
"Factors":{"Factor 1":"PAT15"}
},
{
"Subject ID":"-",
"Sample ID":"BL_29",
"Factors":{"Factor 1":"PAT15"}
},
{
"Subject ID":"-",
"Sample ID":"BL_30",
"Factors":{"Factor 1":"PAT15"}
},
{
"Subject ID":"-",
"Sample ID":"BL_31",
"Factors":{"Factor 1":"PAT15"}
},
{
"Subject ID":"-",
"Sample ID":"BL_32",
"Factors":{"Factor 1":"PAT15"}
},
{
"Subject ID":"-",
"Sample ID":"BL_33",
"Factors":{"Factor 1":"PAT15"}
},
{
"Subject ID":"-",
"Sample ID":"BL_34",
"Factors":{"Factor 1":"PAT15"}
},
{
"Subject ID":"-",
"Sample ID":"BL_35",
"Factors":{"Factor 1":"PAT15"}
},
{
"Subject ID":"-",
"Sample ID":"BL_36",
"Factors":{"Factor 1":"PAT15"}
},
{
"Subject ID":"-",
"Sample ID":"BL_25",
"Factors":{"Factor 1":"PAT23"}
},
{
"Subject ID":"-",
"Sample ID":"BL_26",
"Factors":{"Factor 1":"PAT23"}
},
{
"Subject ID":"-",
"Sample ID":"BL_63",
"Factors":{"Factor 1":"PAT23"}
},
{
"Subject ID":"-",
"Sample ID":"BL_64",
"Factors":{"Factor 1":"PAT23"}
},
{
"Subject ID":"-",
"Sample ID":"BL_65",
"Factors":{"Factor 1":"PAT23"}
},
{
"Subject ID":"-",
"Sample ID":"BL_66",
"Factors":{"Factor 1":"PAT23"}
},
{
"Subject ID":"-",
"Sample ID":"BL_67",
"Factors":{"Factor 1":"PAT23"}
},
{
"Subject ID":"-",
"Sample ID":"BL_1",
"Factors":{"Factor 1":"PAT42"}
},
{
"Subject ID":"-",
"Sample ID":"BL_11",
"Factors":{"Factor 1":"PAT42"}
},
{
"Subject ID":"-",
"Sample ID":"BL_12",
"Factors":{"Factor 1":"PAT42"}
},
{
"Subject ID":"-",
"Sample ID":"BL_13",
"Factors":{"Factor 1":"PAT42"}
},
{
"Subject ID":"-",
"Sample ID":"BL_14",
"Factors":{"Factor 1":"PAT42"}
},
{
"Subject ID":"-",
"Sample ID":"BL_15",
"Factors":{"Factor 1":"PAT42"}
},
{
"Subject ID":"-",
"Sample ID":"BL_16",
"Factors":{"Factor 1":"PAT42"}
},
{
"Subject ID":"-",
"Sample ID":"BL_2",
"Factors":{"Factor 1":"PAT42"}
},
{
"Subject ID":"-",
"Sample ID":"BL_3",
"Factors":{"Factor 1":"PAT42"}
},
{
"Subject ID":"-",
"Sample ID":"BL_4",
"Factors":{"Factor 1":"PAT42"}
},
{
"Subject ID":"-",
"Sample ID":"BL_5",
"Factors":{"Factor 1":"PAT42"}
},
{
"Subject ID":"-",
"Sample ID":"BL_59",
"Factors":{"Factor 1":"PAT42"}
},
{
"Subject ID":"-",
"Sample ID":"BL_6",
"Factors":{"Factor 1":"PAT42"}
},
{
"Subject ID":"-",
"Sample ID":"BL_60",
"Factors":{"Factor 1":"PAT42"}
},
{
"Subject ID":"-",
"Sample ID":"BL_61",
"Factors":{"Factor 1":"PAT42"}
},
{
"Subject ID":"-",
"Sample ID":"BL_62",
"Factors":{"Factor 1":"PAT42"}
},
{
"Subject ID":"-",
"Sample ID":"BL_55",
"Factors":{"Factor 1":"PAT70"}
},
{
"Subject ID":"-",
"Sample ID":"BL_56",
"Factors":{"Factor 1":"PAT70"}
},
{
"Subject ID":"-",
"Sample ID":"BL_57",
"Factors":{"Factor 1":"PAT70"}
},
{
"Subject ID":"-",
"Sample ID":"BL_58",
"Factors":{"Factor 1":"PAT70"}
},
{
"Subject ID":"-",
"Sample ID":"BL_85",
"Factors":{"Factor 1":"Resoration-Control"}
},
{
"Subject ID":"-",
"Sample ID":"BL_86",
"Factors":{"Factor 1":"Resoration-Control"}
},
{
"Subject ID":"-",
"Sample ID":"BL_9",
"Factors":{"Factor 1":"Resoration-Control"}
},
{
"Subject ID":"-",
"Sample ID":"BL_82",
"Factors":{"Factor 1":"Resoration-PAT"}
},
{
"Subject ID":"-",
"Sample ID":"BL_83",
"Factors":{"Factor 1":"Resoration-PAT"}
},
{
"Subject ID":"-",
"Sample ID":"BL_84",
"Factors":{"Factor 1":"Resoration-PAT"}
},
{
"Subject ID":"-",
"Sample ID":"BLP_10",
"Factors":{"Factor 1":"Total Pool"}
},
{
"Subject ID":"-",
"Sample ID":"BLP_11",
"Factors":{"Factor 1":"Total Pool"}
},
{
"Subject ID":"-",
"Sample ID":"BLP_12",
"Factors":{"Factor 1":"Total Pool"}
},
{
"Subject ID":"-",
"Sample ID":"BLP_14",
"Factors":{"Factor 1":"Total Pool"}
},
{
"Subject ID":"-",
"Sample ID":"BLP_15",
"Factors":{"Factor 1":"Total Pool"}
},
{
"Subject ID":"-",
"Sample ID":"BLP_16",
"Factors":{"Factor 1":"Total Pool"}
},
{
"Subject ID":"-",
"Sample ID":"BLP_17",
"Factors":{"Factor 1":"Total Pool"}
},
{
"Subject ID":"-",
"Sample ID":"BLP_18",
"Factors":{"Factor 1":"Total Pool"}
},
{
"Subject ID":"-",
"Sample ID":"BLP_2",
"Factors":{"Factor 1":"Total Pool"}
},
{
"Subject ID":"-",
"Sample ID":"BLP_3",
"Factors":{"Factor 1":"Total Pool"}
},
{
"Subject ID":"-",
"Sample ID":"BLP_4",
"Factors":{"Factor 1":"Total Pool"}
},
{
"Subject ID":"-",
"Sample ID":"BLP_5",
"Factors":{"Factor 1":"Total Pool"}
},
{
"Subject ID":"-",
"Sample ID":"BLP_6",
"Factors":{"Factor 1":"Total Pool"}
},
{
"Subject ID":"-",
"Sample ID":"BLP_8",
"Factors":{"Factor 1":"Total Pool"}
},
{
"Subject ID":"-",
"Sample ID":"BLP_9",
"Factors":{"Factor 1":"Total Pool"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"livers were collected via standard operating procedures .","SAMPLE_TYPE":"Liver","STORAGE_CONDITIONS":"-80℃"},

"TREATMENT":{"TREATMENT_SUMMARY":"PAT15= NOD mice received antibiotics and sacrificed at age of day at 15 ; Control-15=NOD mice received no antibiotics and sacrificed at age of day at 15 ; PAT23= NOD mice received antibiotics and sacrificed at age of day at 23 ; Control-23=NOD mice received no antibiotics and sacrificed at age of day at 23 ; PAT42= NOD mice received antibiotics and sacrificed at age of day at 42 ; Control-42=NOD mice received no antibiotics and sacrificed at age of day at 42 ; PAT70= NOD mice received antibiotics and sacrificed at age of day at 70 ; Control-70=NOD mice received no antibiotics and sacrificed at age of day a t 70; Restoration-PAT= C57 mice received poo from NOD mice give n antibiotics Restoration-Control= C57 mice received poo from NOD mice given n o antibiotics Comments Treatment (Abiotic, Biotic, Intervention) treate d with antibiotics at 5 to 10 days vehicle treated with antibiotics at 5 to 1 0 days vehicle treated with antibiotics at 5 to 10 days vehicle treated wit h antibiotics at 5 to 10 days vehicle Treated with poo from NOD mice give n antibiotics. Treated with poo from NOD mice given vehicle ."},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"Extraction, Solvent Removal, Resuspension, Solvent Removal, Two-ste p Derivatization and Addition of FAME Marker s","PROCESSING_METHOD":"Liver tissue were frozen on dry ice and weighed at approximate 100 mg to a MagNa Lyser tube with 10 to 15 ceramic beads inside. The ice-cold homogenization buffer (50% acetonitrile) was added with the mass/volume ratio at 1 mg tissue per 5 µL buffer. The homogenization was carried on at 4,500 rpm for two 30 sec pulses by the MagNA Lyser. The homogenized mixture was centrifuged at 14,000 rpm for 5 min at -4 °C for the supernatant. Aliquots of 100 µL homogenized supernatant of the study sample (equal to 20 mg tissue) were mixed with 1000 µL of cold degassed 3:3:2 ACN:ISP:H20 solution in a 2 mL snap cap tube. Samples are vortex and shaken for 5 min, and then centrifuged at 4 °C for 2 min at 14000 rcf. The supernatant was split into (2)-450 µL fractions, one fraction was archived in -80°C the second fraction was subject t complete sample processing. Transfer supernatant to a new vial. Evaporate supernatant to complete dryness at room temp.","PROCESSING_STORAGE_CONDITIONS":"On ice","EXTRACTION_METHOD":"(step 1) 3:3:2 Acetonitrile:Isopropanol:H2O, (step 2) 1:1 Acetonitrile:H2O","EXTRACT_STORAGE":"-80℃","SAMPLE_RESUSPENSION":"Samples resuspended in 200 µL of 1:1 ACN:H2O. Evaporated to dryness w/speed vac.","SAMPLE_DERIVATIZATION":"Formation of methoximes by adding 10µL of 40mg/mL MeOx in pyridine to each sample. Placed onto Thermomixer for 90 min at 30⁰C. Then FAME retention index markers and MSTFA added to each sample for derivatization step. Samples returned to Thermomixer for 45 min at 70⁰C.","SAMPLE_SPIKING":"Fatty acid methyl esters (FAME)"},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_SUMMARY":"GCMS analysis is based on the Oliver Fiehn metho d","CHROMATOGRAPHY_TYPE":"GC","INSTRUMENT_NAME":"Leco Pegasus 4D GC","COLUMN_NAME":"Restek Rtx-5Sil MS (30 x 0.25mm, 0.25um)","FLOW_GRADIENT":"constant flow","FLOW_RATE":"1 mL/min","COLUMN_TEMPERATURE":"Initial Oven Temp 100⁰C, hold 60 sec. Ramp rate 20⁰C/min to 330⁰C, hold 5 min.","COLUMN_PRESSURE":"14.05psi","INJECTION_TEMPERATURE":"250⁰C","RETENTION_INDEX":"FAME retention index markers C8-C30","SAMPLE_INJECTION":"1.0 µL","ANALYTICAL_TIME":"20 min","OVEN_TEMPERATURE":"Initial Oven Temp100⁰C, hold 60 sec. Ramp rate 20⁰C/min to 330⁰C, hold 5 min.","TRANSFERLINE_TEMPERATURE":"280⁰C"},

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

"MS":{"MS_COMMENTS":"-","INSTRUMENT_NAME":"Leco Pegasus 4D GCxGC TOF","INSTRUMENT_TYPE":"GC x GC-TOF","MS_TYPE":"EI","ION_MODE":"POSITIVE","HELIUM_FLOW":"1 mL/min","ION_SOURCE_TEMPERATURE":"250⁰C","IONIZATION_ENERGY":"70eV","SOURCE_TEMPERATURE":"250⁰C","DATAFORMAT":"netcdf","RESOLUTION_SETTING":"1200","SCAN_RANGE_MOVERZ":"50-750","SCANNING":"20 spectra/sec","MS_RESULTS_FILE":"ST000962_AN001576_Results.txt UNITS:m/z"},

"MS_METABOLITE_DATA":{
"Units":"m/z",

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