{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST000481","ANALYSIS_ID":"AN001449","VERSION":"1","CREATED_ON":"November 3, 2017, 2:09 pm"},

"PROJECT":{"PROJECT_TITLE":"Metabolomics of Mice Cohousing and Microbiota Transfer","PROJECT_SUMMARY":"Metabolomics analysis was performed on twelve mice serum samples from Dr. Martin Blaser's laboratory at NYU school of medicine. Serum from week 15 mice were analyzed: (a) mice received low-dose antibiotics until week 4 (STAT), (b) mice received no antibiotics (control), (c) mice received low dose antibiotics (STAT) and then cohoused with control animals (STAT-coho), (d) mice received no antibiotics and then were cohoused with STAT animals (Control-coho). In this collaboration, we are interested in the metabolic differences among these groups","INSTITUTE":"New York University","DEPARTMENT":"Langone Medical Center Langone Medical Center","LAST_NAME":"Blaser","FIRST_NAME":"Martin","ADDRESS":"550 First Avenue, BCD 689, New York, NY 10016","EMAIL":"Martin.Blaser@nyumc.org","PHONE":"646-501-4386"},

"STUDY":{"STUDY_TITLE":"Metabolomics of Mice Cohousing and Microbiota Transfer (part II)","STUDY_SUMMARY":"The mice serum samples were extracted and analyzed using broad spectrum GCMS for the identification of compounds distinguishing the groups.","INSTITUTE":"RTI International","DEPARTMENT":"RCMRC","LABORATORY":"NIH Eastern Regional Comprehensive Metabolomics Resource Core (RTI RCMRC)","LAST_NAME":"Sumner","FIRST_NAME":"Susan","ADDRESS":"3040 E Cornwallis Road, Research Triangle Park, NC 27709","EMAIL":"ssumner@rti.org","PHONE":"919-541-7479","NUM_GROUPS":"4","TOTAL_SUBJECTS":"12"},

"SUBJECT":{"SUBJECT_TYPE":"Animal","SUBJECT_SPECIES":"Mus musculus","TAXONOMY_ID":"10090"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"-",
"Sample ID":"C94",
"Factors":{"Group":"Control"},
"Additional sample data":{"Datafile Name":"150807ajcsa08"}
},
{
"Subject ID":"-",
"Sample ID":"S58",
"Factors":{"Group":"STAT-COHO"},
"Additional sample data":{"Datafile Name":"150807ajcsa09"}
},
{
"Subject ID":"-",
"Sample ID":"C36",
"Factors":{"Group":"Control-COHO"},
"Additional sample data":{"Datafile Name":"150807ajcsa10"}
},
{
"Subject ID":"-",
"Sample ID":"S111",
"Factors":{"Group":"Stat"},
"Additional sample data":{"Datafile Name":"150807ajcsa11"}
},
{
"Subject ID":"-",
"Sample ID":"TP01",
"Factors":{"Group":"Study Total Pool"},
"Additional sample data":{"Datafile Name":"150807ajcsa12"}
},
{
"Subject ID":"-",
"Sample ID":"ExTP2",
"Factors":{"Group":"External Study Pool"},
"Additional sample data":{"Datafile Name":"150807ajcsa13"}
},
{
"Subject ID":"-",
"Sample ID":"TP02",
"Factors":{"Group":"Study Total Pool"},
"Additional sample data":{"Datafile Name":"150807ajcsa14"}
},
{
"Subject ID":"-",
"Sample ID":"C42",
"Factors":{"Group":"Control-COHO"},
"Additional sample data":{"Datafile Name":"150807ajcsa15"}
},
{
"Subject ID":"-",
"Sample ID":"C97",
"Factors":{"Group":"Control"},
"Additional sample data":{"Datafile Name":"150807ajcsa16"}
},
{
"Subject ID":"-",
"Sample ID":"S54",
"Factors":{"Group":"Stat"},
"Additional sample data":{"Datafile Name":"150807ajcsa17"}
},
{
"Subject ID":"-",
"Sample ID":"ExTP1",
"Factors":{"Group":"External Study Pool"},
"Additional sample data":{"Datafile Name":"150807ajcsa19"}
},
{
"Subject ID":"-",
"Sample ID":"C35",
"Factors":{"Group":"Control-COHO"},
"Additional sample data":{"Datafile Name":"150807ajcsa20"}
},
{
"Subject ID":"-",
"Sample ID":"S60",
"Factors":{"Group":"STAT-COHO"},
"Additional sample data":{"Datafile Name":"150807ajcsa21"}
},
{
"Subject ID":"-",
"Sample ID":"S104",
"Factors":{"Group":"Stat"},
"Additional sample data":{"Datafile Name":"150807ajcsa22"}
},
{
"Subject ID":"-",
"Sample ID":"C38",
"Factors":{"Group":"Control"},
"Additional sample data":{"Datafile Name":"150807ajcsa23"}
},
{
"Subject ID":"-",
"Sample ID":"S56",
"Factors":{"Group":"STAT-COHO"},
"Additional sample data":{"Datafile Name":"150807ajcsa24"}
},
{
"Subject ID":"-",
"Sample ID":"ExTP3",
"Factors":{"Group":"External Study Pool"},
"Additional sample data":{"Datafile Name":"150807ajcsa25"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"Serum was collected via standard operating procedures.","SAMPLE_TYPE":"blood","STORAGE_CONDITIONS":"-80 °C","BLOOD_SERUM_OR_PLASMA":"Serum"},

"TREATMENT":{"TREATMENT_SUMMARY":"STAT | Control | STAT-COHO | Control-COHO","TREATMENT_PROTOCOL_COMMENTS":"STAT treated mice were cohoused with Control mice | Control mice were cohoused with STAT treated mice","TREATMENT_COMPOUND":"low dose antibiotics until week 4 | no antibiotics"},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"Extraction, Solvent Removal, Resuspension, Solvent Removal, Two-step Derivatization and Addition of FAME Markers","PROCESSING_METHOD":"30 µL of serum were added to Eppendorf tube. Add 1000 µL of 3:3:2 ACN:ISP:H20 extraction solution to aliquots, shake and centrifuge for 2 minutes at 4C and 14000 rcf to precipitate proteins. Sample 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 and or 4⁰C cold room","EXTRACTION_METHOD":"(step 1) 3:3:2 Acetonitrile:Isopropanol:H2O, (step 2) 1:1 Acetonitrile:H2O","EXTRACT_STORAGE":"-80⁰C","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 method","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","LABORATORY_NAME":"NIH Eastern Regional Comprehensive Metabolomics Resource Core (RTI RCMRC)","OPERATOR_NAME":"James Carlson","ACQUISITION_DATE":"8/7/2015","DATA_FORMAT":"NETCDF"},

"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","RESOLUTION_SETTING":"1200","SCAN_RANGE_MOVERZ":"50-750","SCANNING":"20 spectra/sec","MS_RESULTS_FILE":"ST000481_AN001449_Results.txt UNITS:intensity"},

"MS_METABOLITE_DATA":{
"Units":"intensity",

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