{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST000032","ANALYSIS_ID":"AN000052","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(NOD-Cecal)","STUDY_TYPE":"Metabolomics","STUDY_SUMMARY":"In the NOD sub-study, a total of 18 samples from 6 week old, male NOD/ShiLtj mice; comprised of 6 serum samples, 6 cecal content samples and 6 liver tissue samples were analyzed.  Three mice/matrix were exposed to PAT and 3 mice/matrix were non-exposed Controls. The mice were housed with SPF (Helicobacter neg/MNV neg) bedding and fed a normal 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":"NOD_Cecal Study","PHONE":"-","ADDRESS":"-"},

"SUBJECT":{"SUBJECT_TYPE":"Animal","SUBJECT_SPECIES":"Mus musculus","TAXONOMY_ID":"10090","GENOTYPE_STRAIN":"NOD/ShiLtj","GENDER":"Male","ANIMAL_ANIMAL_SUPPLIER":"Jackson Laboratories","ANIMAL_HOUSING":"SPF (Helicobacter neg / MNV neg)","ANIMAL_FEED":"normal chow","SPECIES_GROUP":"Mammal"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"-",
"Sample ID":"CNC111",
"Factors":{"Treatment Group":"Control"}
},
{
"Subject ID":"-",
"Sample ID":"CNC140",
"Factors":{"Treatment Group":"Control"}
},
{
"Subject ID":"-",
"Sample ID":"CNC141",
"Factors":{"Treatment Group":"Control"}
},
{
"Subject ID":"-",
"Sample ID":"CNP124",
"Factors":{"Treatment Group":"PAT"}
},
{
"Subject ID":"-",
"Sample ID":"CNP126",
"Factors":{"Treatment Group":"PAT"}
},
{
"Subject ID":"-",
"Sample ID":"CNP127",
"Factors":{"Treatment Group":"PAT"}
},
{
"Subject ID":"-",
"Sample ID":"CPL101",
"Factors":{"Treatment Group":"Pool QC"}
},
{
"Subject ID":"-",
"Sample ID":"CPL102",
"Factors":{"Treatment Group":"Pool QC"}
},
{
"Subject ID":"-",
"Sample ID":"CPL103",
"Factors":{"Treatment Group":"Pool QC"}
},
{
"Subject ID":"-",
"Sample ID":"CPL201",
"Factors":{"Treatment Group":"Pool QC"}
},
{
"Subject ID":"-",
"Sample ID":"CPL202",
"Factors":{"Treatment Group":"Pool QC"}
},
{
"Subject ID":"-",
"Sample ID":"CPL203",
"Factors":{"Treatment Group":"Pool QC"}
}
],
"COLLECTION":{"SAMPLE_TYPE":"cecal contents","COLLECTION_TIME":"6 weeks","COLLECTION_SUMMARY":"-"},

"TREATMENT":{"TREATMENT_SUMMARY":"Three mice were exposed to PAT and 3 mice were non-exposed controls. PAT= therapeutic dose-pulsed antibiotic treatment.","TREATMENT_COMPOUND":"PAT"},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"Frozen cecal contents (cecal) samples were weighed into labeled homogenizer bead tubes.  D20 was added to each tube (500 µL if less than 50 mg and 1000 µL if more than 100 mg of tissue).  The samples were homogenized on a Spex Geno/Grinder for two 30 second pulses at 1750 rpm.  Samples were centrifuged at 12000 rcf for 5 min.  Cecal supernatants were transferred (450/700 µL) into 2.0 mL 0.2 µm nylon filter tubes and centrifuged at 16000 rcf until all the homogenate was filtered.  The 200 µL remaining aliquot from each 1000 µL cecal sample was combined in a 10 mL tube and vortexed for 30 seconds to generate pooled samples for QC during analysis. Three “low” QC pools were generated by transferring 450 µL of the pooled homogenate into 2.0 mL 0.2 µm nylon filter tubes; and three “high” QC pools were generated by transferring 700 µL of the pooled homogenate into 2.0 mL 0.2 µm nylon filter tubes and also centrifuged at 16000 rcf until all the homogenate was filtered. The volume of homogenate needed to analyze 50 mg/sample and volume of D20 needed to bring the total volume to 630 µL was calculated.  The calculated volumes of filtered supernatant and D20 were then transferred into BSI-labeled tubes. 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.  Samples were vortexed for 30 seconds and centrifuged at 12000 rcf for 5 minutes.  A 600 µL aliquot of the supernatant was then transferred into 5mm NMR tubes (Wilmad LabGlass, New Jersey, USA) which were kept on ice until data acquisition.","SAMPLEPREP_PROTOCOL_FILENAME":"NOD_Cecal_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":"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":"10","OFFSET_FREQUENCY":"3293 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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