{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST000036","ANALYSIS_ID":"AN000056","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(EstroSTAT-Serum)","STUDY_TYPE":"Metabolomics","STUDY_SUMMARY":"In the EstroSTAT sub-study, a total of 18 samples from 23 week old, female C57BL/6 mice; comprised of 6 urine samples, 6 serum 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 Low phyto-estrogen 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":"EstroSTAT_Serum","PHONE":"-","ADDRESS":"-"},

"SUBJECT":{"SUBJECT_TYPE":"Animal","SUBJECT_SPECIES":"Mus musculus","TAXONOMY_ID":"10090","GENOTYPE_STRAIN":"C57BL/6","GENDER":"Female","ANIMAL_HOUSING":"Conventional","ANIMAL_FEED":"Low phyto-estrogen diet","SPECIES_GROUP":"Mammal"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"-",
"Sample ID":"SEC906",
"Factors":{"Treatment Group":"Control"}
},
{
"Subject ID":"-",
"Sample ID":"SEC920",
"Factors":{"Treatment Group":"Control"}
},
{
"Subject ID":"-",
"Sample ID":"SEC922",
"Factors":{"Treatment Group":"Control"}
},
{
"Subject ID":"-",
"Sample ID":"SPL101",
"Factors":{"Treatment Group":"Pooled QC"}
},
{
"Subject ID":"-",
"Sample ID":"SPL102",
"Factors":{"Treatment Group":"Pooled QC"}
},
{
"Subject ID":"-",
"Sample ID":"SPL103",
"Factors":{"Treatment Group":"Pooled QC"}
},
{
"Subject ID":"-",
"Sample ID":"SES365",
"Factors":{"Treatment Group":"STAT"}
},
{
"Subject ID":"-",
"Sample ID":"SES910",
"Factors":{"Treatment Group":"STAT"}
},
{
"Subject ID":"-",
"Sample ID":"SES911",
"Factors":{"Treatment Group":"STAT"}
}
],
"COLLECTION":{"SAMPLE_TYPE":"blood","COLLECTION_TIME":"23 weeks","BLOOD_SERUM_OR_PLASMA":"serum","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 serum study samples were thawed on ice and vortexed for 30 seconds. Aliquots of 50/100 µL (sub-study dependent) were transferred into BSI-labeled eppendorf tubes. Purchased mouse sera (Sigma #S7273) was also transferred into three BSI-labeled eppendorf tubes (50/100 µL) for QC samples during analysis. Freshly prepared 0.9% Saline (wt/v) solution in 10% D2O, was added to each tube (150/100 µL) and they were vortexed for 30 seconds. Freshly prepared 10 mM Formate solution containing 2% (wt/v) NaN3 was added to each tube (50 µL) to serve as internal standard and they were vortexed for 30 seconds again, then centrifuged at 12000 rcf for 5 minutes at 4 °C. A 200 µL aliquot of the supernatant was transferred into 3 mm NMR tubes (Bruker-Biospin, Germany), which were kept on ice until data acquisition.","SAMPLEPREP_PROTOCOL_FILENAME":"EstroSTAT_Serum_Metabolomics_Procedure.docx"},

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

"ANALYSIS":{"LABORATORY_NAME":"RTI/ DHHMRI","ANALYSIS_TYPE":"NMR","ACQUISITION_DATE":"41527","SOFTWARE_VERSION":"Top Spin 3.2","OPERATOR_NAME":"Wimal Pathmasiri/ Kevin Knagge/ Jason Winnikie","DETECTOR_TYPE":"NMR","DATA_FORMAT":"NMR"},

"NM":{"INSTRUMENT_TYPE":"Bruker Avance III","NMR_EXPERIMENT_TYPE":"1D 1H","FIELD_FREQUENCY_LOCK":"Deuterium","STANDARD_CONCENTRATION":"1.0 mM","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":"cpmgpr1d","WATER_SUPPRESSION":"presat","PULSE_WIDTH":"14.84 us","POWER_LEVEL":"25.704w","RECEIVER_GAIN":"4.5","OFFSET_FREQUENCY":"3300.70 Hz","CHEMICAL_SHIFT_REF_CPD":"Formate","TEMPERATURE":"298.1 K","NUMBER_OF_SCANS":"512","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":"Formate","INSTRUMENT_NAME":"Bruker Avance III"},

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