{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST000028","ANALYSIS_ID":"AN000048","VERSION":"1","CREATED_ON":"10-02-2015"},

"PROJECT":{"PROJECT_TITLE":"Metabolomics Involved in Early Life Antibiotic Exposures","PROJECT_TYPE":"Obesity modeling of antibiotic exposure","PROJECT_SUMMARY":"The project Metabolomics Involved in Early Life Antibiotic Exposures profiled a total of 90 samples from five sub-studies (DuraSTAT, TranSTAT, NOD, EstroSTAT and VG STAT) which included a total of four sample matrices (urine, serum, liver tissue and cecal contents). Within each sub-study, there were three sample matrices except for VG STAT, for which there was only two. For each matrix type within each sub-study 6 samples were analyzed for a total of 18 samples per sub-study (9 of each in VG STAT), the samples were equally divided into STAT/PAT-treated (sub-therapeutic antibiotic treatment (STAT) and therapeutic dose-pulsed antibiotic treatment (PAT)) collected at various time-points versus untreated Controls for each matrix.","INSTITUTE":"New York University","DEPARTMENT":"School of Medicine","LABORATORY":"Blaser Laboratory","LAST_NAME":"Blaser","FIRST_NAME":"Martin J.","ADDRESS":"550 First Avenue, BCD 690, New York, NY 10016","EMAIL":"Martin.Blaser@nyumc.org","PUBLICATIONS":"Cho I, Blaser MJ. The human microbiome: at the interface of health and disease. Nature Reviews. Genetics 2012; 13; 260-270","PHONE":"-"},

"STUDY":{"STUDY_TITLE":"Metabolomics Involved in Early Life Antibiotic Exposures(DuraSTAT-Urine)","STUDY_TYPE":"Metabolomics","STUDY_SUMMARY":"In the DuraSTAT sub-study, a total of 18 samples from 8 week old, female C57BL/6 mice; comprised of 6 urine samples, 6 cecal content samples and 6 liver tissue samples were analyzed. Three mice/matrix were given STAT penicillin and 3 mice/matrix were non-treated Controls. The mice were housed with conventional bedding and fed a high fat diet.","INSTITUTE":"RTI International","DEPARTMENT":"Systems and Translational Sciences (STS)","LABORATORY":"NIH Eastern Regional Comprehensive Metabolomics Resource Core (RTI RCMRC)","LAST_NAME":"Sumner","FIRST_NAME":"Susan","EMAIL":"ssumner@rti.org","NUM_GROUPS":"2","TOTAL_SUBJECTS":"6","STUDY_COMMENTS":"DuraSTAT_Urine","PHONE":"-","ADDRESS":"-"},

"SUBJECT":{"SUBJECT_TYPE":"Animal","SUBJECT_SPECIES":"Mus musculus","TAXONOMY_ID":"10090","GENOTYPE_STRAIN":"C57BL/6","AGE_OR_AGE_RANGE":"8 weeks at collection","GENDER":"Female","ANIMAL_ANIMAL_SUPPLIER":"Jackson Labs","ANIMAL_HOUSING":"Conventional","ANIMAL_FEED":"High Fat Diet","SPECIES_GROUP":"Mammal"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"-",
"Sample ID":"UDC029",
"Factors":{"Treatment Group":"Control"}
},
{
"Subject ID":"-",
"Sample ID":"UDC030",
"Factors":{"Treatment Group":"Control"}
},
{
"Subject ID":"-",
"Sample ID":"UDC032",
"Factors":{"Treatment Group":"Control"}
},
{
"Subject ID":"-",
"Sample ID":"UPL101",
"Factors":{"Treatment Group":"Pool QC"}
},
{
"Subject ID":"-",
"Sample ID":"UPL102",
"Factors":{"Treatment Group":"Pool QC"}
},
{
"Subject ID":"-",
"Sample ID":"UPL103",
"Factors":{"Treatment Group":"Pool QC"}
},
{
"Subject ID":"-",
"Sample ID":"UDS039",
"Factors":{"Treatment Group":"STAT"}
},
{
"Subject ID":"-",
"Sample ID":"UDS052",
"Factors":{"Treatment Group":"STAT"}
},
{
"Subject ID":"-",
"Sample ID":"UDS054",
"Factors":{"Treatment Group":"STAT"}
}
],
"COLLECTION":{"SAMPLE_TYPE":"urine","COLLECTION_TIME":"8 weeks","COLLECTION_SUMMARY":"-"},

"TREATMENT":{"TREATMENT_SUMMARY":"Three mice were given STAT penicillin and 3 mice were non-treated controls. STAT = sub-therapeutic antibiotic treatment.","TREATMENT_COMPOUND":"STAT penicillin"},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"Frozen urine study samples were thawed on ice and vortexed for 30 seconds. Aliquots of 400 µL were transferred into BSI-labeled eppendorf tubes. Aliquots of 100 µL per study sample were also transferred into a 10 mL tube to generate pooled samples for QC during analysis, and 400 µL was transferred into BSI-labeled eppendorf tubes. D2O (230 µL) was added to each tube.  Chenomx Internal Standard solution (Chenomx ISTD, Edmonton, Alberta, Canada) contains 5mM 4,4-dimethyl-4-silapentane-1-sulfonic acid (DSS, Chemical Shift Indicator), 100 mM Imidazole (pH indicator), and 0.2% NaN3 (to inhibit bacterial growth) was added (70 µl) to the tubes. Tubes were vortexed for 30 seconds and centrifuged at 12000 rcf for 5min. A 600 µL aliquot of the supernatant was transferred into 5mm NMR tubes (Bruker-Biospin, Germany), which were kept on ice until data acquisition.","SAMPLEPREP_PROTOCOL_FILENAME":"DuraSTAT_Urine_Metabolomics_Procedure.docx"},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_TYPE":"-","INSTRUMENT_NAME":"-","COLUMN_NAME":"-"},

"ANALYSIS":{"LABORATORY_NAME":"RTI/ DHHMRI","ANALYSIS_TYPE":"NMR","ACQUISITION_DATE":"41522","SOFTWARE_VERSION":"Top Spin 3.2","OPERATOR_NAME":"Wimal Pathmasiri/ Kevin Knagge/ Jason Winnikie","DETECTOR_TYPE":"NMR","DATA_FORMAT":"NMR"},

"NM":{"INSTRUMENT_TYPE":"Bruker","NMR_EXPERIMENT_TYPE":"1D 1H","FIELD_FREQUENCY_LOCK":"Deuterium","STANDARD_CONCENTRATION":"0.5mM","SPECTROMETER_FREQUENCY":"700 MHz","NMR_PROBE":"cyrogenically cooled ATMA inverse probe","NMR_SOLVENT":"D2O","NMR_TUBE_SIZE":"5mm x 4inch","SHIMMING_METHOD":"topshim","PULSE_SEQUENCE":"noesypr1d","WATER_SUPPRESSION":"presat","PULSE_WIDTH":"14.84 us","POWER_LEVEL":"25.704w","RECEIVER_GAIN":"4","OFFSET_FREQUENCY":"3293.10 Hz","CHEMICAL_SHIFT_REF_CPD":"DSS","TEMPERATURE":"298.1 K","NUMBER_OF_SCANS":"64","DUMMY_SCANS":"4","ACQUISITION_TIME":"2.3243434","RELAXATION_DELAY":"2 s","SPECTRAL_WIDTH":"20.1358","NUM_DATA_POINTS_ACQUIRED":"65536","REAL_DATA_POINTS":"65536","LINE_BROADENING":"0.5","ZERO_FILLING":"yes","APODIZATION":"lorentzian","BASELINE_CORRECTION_METHOD":"polynomial","CHEMICAL_SHIFT_REF_STD":"DSS","INSTRUMENT_NAME":"Bruker Avance III"},

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