{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST001649","ANALYSIS_ID":"AN002695","VERSION":"1","CREATED_ON":"January 13, 2021, 10:27 am"},

"PROJECT":{"PROJECT_TITLE":"Urinary microbiota and metabolome in pediatric vesicoureteral reflux and scarring","PROJECT_TYPE":"Observational/cross-sectional","PROJECT_SUMMARY":"Experiment to analyze the changes in the urinary microbiota and metabolome related to pediatric veicoureteral reflux with special attention to the differences related to renal scarring.","INSTITUTE":"University of Missouri-Columbia","DEPARTMENT":"Surgery","LAST_NAME":"Malm-Buatsi","FIRST_NAME":"Elizabeth","ADDRESS":"1 Hospital Dr, MC 301, Columbia, MO 65212","EMAIL":"malmbuatsie@health.missouri.edu","PHONE":"(573) 817-3311"},

"STUDY":{"STUDY_TITLE":"Urinary microbiota and metabolome in pediatric vesicoureteral reflux and scarring","STUDY_TYPE":"Observational/cross-sectional","STUDY_SUMMARY":"We enrolled girls and boys aged zero to nine years presenting to a pediatric urologist for recurrent urinary tract infection (UTI) or renal scarring (decreased uptake on a nuclear renal scan) or grade 3-5 vesico ureteral reflux (VUR). Exclusion criteria included other urogenital abnormalities, medical renal disease, immunodeficiency, syndromes associated with VUR, acute UTI, persistent UTI (ongoing positive urine culture 1-3 weeks after completing a treatment course), or global renal atrophy on imaging. At one patient visit, a urine specimen was collected for 16S and metabolomic analysis.","INSTITUTE":"University of Missouri-Columbia","DEPARTMENT":"MU Metabolomics Center","LAST_NAME":"Sarma","FIRST_NAME":"Saurav","ADDRESS":"1201 Rollins street, Bond Life Science Center","EMAIL":"sarmas@missouri.edu","PHONE":"5738825596"},

"SUBJECT":{"SUBJECT_TYPE":"Human","SUBJECT_SPECIES":"Homo sapiens","TAXONOMY_ID":"9606","AGE_OR_AGE_RANGE":"4.14 to 8.86 years","WEIGHT_OR_WEIGHT_RANGE":"4.5 to 41.3 kg","HEIGHT_OR_HEIGHT_RANGE":"56.0 to 143.1 inch","GENDER":"Male and female","HUMAN_RACE":"white"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"-",
"Sample ID":"A10",
"Factors":{"race":"White","sex":"F","category":"No scarring"},
"Additional sample data":{"age_at_collection(years)":"5.115068493","weight(kg)":"18.2","height(cm)":"108","RAW_FILE_NAME":"A-10.D"}
},
{
"Subject ID":"-",
"Sample ID":"B1",
"Factors":{"race":"White","sex":"F","category":"No VUR"},
"Additional sample data":{"age_at_collection(years)":"4.520547945","weight(kg)":"17.8","height(cm)":"106","RAW_FILE_NAME":"B-1.D"}
},
{
"Subject ID":"-",
"Sample ID":"B3",
"Factors":{"race":"White","sex":"M","category":"No VUR"},
"Additional sample data":{"age_at_collection(years)":"0.243835616","weight(kg)":"6.1","height(cm)":"-","RAW_FILE_NAME":"B-3.D"}
},
{
"Subject ID":"-",
"Sample ID":"B4",
"Factors":{"race":"White","sex":"F","category":"No VUR"},
"Additional sample data":{"age_at_collection(years)":"1.287671233","weight(kg)":"9.3","height(cm)":"-","RAW_FILE_NAME":"B-4.D"}
},
{
"Subject ID":"-",
"Sample ID":"B5",
"Factors":{"race":"White","sex":"F","category":"No VUR"},
"Additional sample data":{"age_at_collection(years)":"4.975342466","weight(kg)":"16.7","height(cm)":"106.8","RAW_FILE_NAME":"B-5.D"}
},
{
"Subject ID":"-",
"Sample ID":"B6",
"Factors":{"race":"White","sex":"F","category":"No VUR"},
"Additional sample data":{"age_at_collection(years)":"4.868493151","weight(kg)":"18.1","height(cm)":"114.4","RAW_FILE_NAME":"B-6.D"}
},
{
"Subject ID":"-",
"Sample ID":"B7",
"Factors":{"race":"White","sex":"F","category":"No VUR"},
"Additional sample data":{"age_at_collection(years)":"4.797260274","weight(kg)":"15.6","height(cm)":"103","RAW_FILE_NAME":"B-7.D"}
},
{
"Subject ID":"-",
"Sample ID":"B9",
"Factors":{"race":"White","sex":"F","category":"No VUR"},
"Additional sample data":{"age_at_collection(years)":"8.657534247","weight(kg)":"39.3","height(cm)":"134.5","RAW_FILE_NAME":"B-9.D"}
},
{
"Subject ID":"-",
"Sample ID":"B12",
"Factors":{"race":"White","sex":"F","category":"No VUR"},
"Additional sample data":{"age_at_collection(years)":"1.112328767","weight(kg)":"11.6","height(cm)":"76.2","RAW_FILE_NAME":"B-12.D"}
},
{
"Subject ID":"-",
"Sample ID":"B13",
"Factors":{"race":"White","sex":"F","category":"No VUR"},
"Additional sample data":{"age_at_collection(years)":"2.37260274","weight(kg)":"15","height(cm)":"-","RAW_FILE_NAME":"B-13.D"}
},
{
"Subject ID":"-",
"Sample ID":"B15",
"Factors":{"race":"White","sex":"F","category":"No VUR"},
"Additional sample data":{"age_at_collection(years)":"4.942465753","weight(kg)":"22.2","height(cm)":"114.4","RAW_FILE_NAME":"B-15.D"}
},
{
"Subject ID":"-",
"Sample ID":"B16",
"Factors":{"race":"White","sex":"F","category":"No VUR"},
"Additional sample data":{"age_at_collection(years)":"4.575342466","weight(kg)":"25.4","height(cm)":"115","RAW_FILE_NAME":"B-16.D"}
},
{
"Subject ID":"-",
"Sample ID":"A1",
"Factors":{"race":"White","sex":"F","category":"No VUR"},
"Additional sample data":{"age_at_collection(years)":"4.139726027","weight(kg)":"17.2","height(cm)":"-","RAW_FILE_NAME":"A-1.D"}
},
{
"Subject ID":"-",
"Sample ID":"A2",
"Factors":{"race":"White","sex":"F","category":"Scarring"},
"Additional sample data":{"age_at_collection(years)":"4.364383562","weight(kg)":"23.2","height(cm)":"-","RAW_FILE_NAME":"A-2.D"}
},
{
"Subject ID":"-",
"Sample ID":"A3",
"Factors":{"race":"White","sex":"F","category":"No scarring"},
"Additional sample data":{"age_at_collection(years)":"0.498630137","weight(kg)":"7.8","height(cm)":"-","RAW_FILE_NAME":"A-3.D"}
},
{
"Subject ID":"-",
"Sample ID":"A4",
"Factors":{"race":"White","sex":"F","category":"Scarring"},
"Additional sample data":{"age_at_collection(years)":"4.709589041","weight(kg)":"16.3","height(cm)":"-","RAW_FILE_NAME":"A-4.D"}
},
{
"Subject ID":"-",
"Sample ID":"A5",
"Factors":{"race":"White","sex":"F","category":"No scarring"},
"Additional sample data":{"age_at_collection(years)":"0.295890411","weight(kg)":"4.7","height(cm)":"-","RAW_FILE_NAME":"A-5.D"}
},
{
"Subject ID":"-",
"Sample ID":"A6",
"Factors":{"race":"White","sex":"F","category":"Scarring"},
"Additional sample data":{"age_at_collection(years)":"2.720547945","weight(kg)":"13.76","height(cm)":"91","RAW_FILE_NAME":"A-6.D"}
},
{
"Subject ID":"-",
"Sample ID":"A8",
"Factors":{"race":"White","sex":"F","category":"Scarring"},
"Additional sample data":{"age_at_collection(years)":"4.928767123","weight(kg)":"18.5","height(cm)":"-","RAW_FILE_NAME":"A-8.D"}
},
{
"Subject ID":"-",
"Sample ID":"A7",
"Factors":{"race":"White","sex":"F","category":"Scarring"},
"Additional sample data":{"age_at_collection(years)":"7.082191781","weight(kg)":"24.5","height(cm)":"120.7","RAW_FILE_NAME":"A-7.D"}
},
{
"Subject ID":"-",
"Sample ID":"A9",
"Factors":{"race":"White","sex":"F","category":"No scarring"},
"Additional sample data":{"age_at_collection(years)":"6.38630137","weight(kg)":"25.3","height(cm)":"121.5","RAW_FILE_NAME":"A-9.D"}
},
{
"Subject ID":"-",
"Sample ID":"B8",
"Factors":{"race":"White","sex":"F","category":"No scarring"},
"Additional sample data":{"age_at_collection(years)":"0.306849315","weight(kg)":"6.7","height(cm)":"61","RAW_FILE_NAME":"B-8.D"}
},
{
"Subject ID":"-",
"Sample ID":"A11",
"Factors":{"race":"White","sex":"F","category":"No scarring"},
"Additional sample data":{"age_at_collection(years)":"0.079452055","weight(kg)":"4.5","height(cm)":"58","RAW_FILE_NAME":"A-11.D"}
},
{
"Subject ID":"-",
"Sample ID":"A12",
"Factors":{"race":"Black","sex":"F","category":"No scarring"},
"Additional sample data":{"age_at_collection(years)":"5.057534247","weight(kg)":"20.4","height(cm)":"109.6","RAW_FILE_NAME":"A-12.D"}
},
{
"Subject ID":"-",
"Sample ID":"A13",
"Factors":{"race":"White","sex":"F","category":"No scarring"},
"Additional sample data":{"age_at_collection(years)":"4.402739726","weight(kg)":"14.3","height(cm)":"102.8","RAW_FILE_NAME":"A-13.D"}
},
{
"Subject ID":"-",
"Sample ID":"A14",
"Factors":{"race":"White","sex":"F","category":"No scarring"},
"Additional sample data":{"age_at_collection(years)":"4.865753425","weight(kg)":"16.4","height(cm)":"107.3","RAW_FILE_NAME":"A-14.D"}
},
{
"Subject ID":"-",
"Sample ID":"B10",
"Factors":{"race":"White","sex":"F","category":"No VUR"},
"Additional sample data":{"age_at_collection(years)":"8.860273973","weight(kg)":"38.05","height(cm)":"143.1","RAW_FILE_NAME":"B-10.D"}
},
{
"Subject ID":"-",
"Sample ID":"A15",
"Factors":{"race":"White","sex":"F","category":"No scarring"},
"Additional sample data":{"age_at_collection(years)":"2.539726027","weight(kg)":"12.1","height(cm)":"89.5","RAW_FILE_NAME":"A-15.D"}
},
{
"Subject ID":"-",
"Sample ID":"B11",
"Factors":{"race":"White","sex":"M","category":"No scarring"},
"Additional sample data":{"age_at_collection(years)":"0.156164384","weight(kg)":"5.1","height(cm)":"56","RAW_FILE_NAME":"B-11.D"}
},
{
"Subject ID":"-",
"Sample ID":"A16",
"Factors":{"race":"White","sex":"F","category":"No VUR"},
"Additional sample data":{"age_at_collection(years)":"3.520547945","weight(kg)":"14.3","height(cm)":"97.5","RAW_FILE_NAME":"A-16.D"}
},
{
"Subject ID":"-",
"Sample ID":"A17",
"Factors":{"race":"Other","sex":"F","category":"VUR"},
"Additional sample data":{"age_at_collection(years)":"0.849315068","weight(kg)":"10.8","height(cm)":"77.6","RAW_FILE_NAME":"A-17.D"}
},
{
"Subject ID":"-",
"Sample ID":"A18",
"Factors":{"race":"White","sex":"M","category":"Scarring"},
"Additional sample data":{"age_at_collection(years)":"2.205479452","weight(kg)":"12.9","height(cm)":"-","RAW_FILE_NAME":"A-18.D"}
},
{
"Subject ID":"-",
"Sample ID":"B14",
"Factors":{"race":"White","sex":"F","category":"No VUR"},
"Additional sample data":{"age_at_collection(years)":"8.575342466","weight(kg)":"41.3","height(cm)":"133.2","RAW_FILE_NAME":"B-14.D"}
},
{
"Subject ID":"-",
"Sample ID":"A20",
"Factors":{"race":"White","sex":"F","category":"Scarring"},
"Additional sample data":{"age_at_collection(years)":"4.197260274","weight(kg)":"16","height(cm)":"102","RAW_FILE_NAME":"A-20.D"}
},
{
"Subject ID":"-",
"Sample ID":"A22",
"Factors":{"race":"White","sex":"F","category":"No scarring"},
"Additional sample data":{"age_at_collection(years)":"7.553424658","weight(kg)":"20.5","height(cm)":"121.5","RAW_FILE_NAME":"A-22.D"}
},
{
"Subject ID":"-",
"Sample ID":"B17",
"Factors":{"race":"White","sex":"F","category":"No VUR"},
"Additional sample data":{"age_at_collection(years)":"5.317808219","weight(kg)":"18.3","height(cm)":"110.2","RAW_FILE_NAME":"B-17.D"}
},
{
"Subject ID":"-",
"Sample ID":"A23",
"Factors":{"race":"White","sex":"F","category":"No scarring"},
"Additional sample data":{"age_at_collection(years)":"5.043835616","weight(kg)":"18.6","height(cm)":"103.5","RAW_FILE_NAME":"A-23.D"}
},
{
"Subject ID":"-",
"Sample ID":"A24",
"Factors":{"race":"White","sex":"F","category":"No scarring"},
"Additional sample data":{"age_at_collection(years)":"0.350684932","weight(kg)":"5.65","height(cm)":"59.5","RAW_FILE_NAME":"A-24.D"}
},
{
"Subject ID":"-",
"Sample ID":"B18",
"Factors":{"race":"White","sex":"F","category":"No scarring"},
"Additional sample data":{"age_at_collection(years)":"2.117808219","weight(kg)":"14.6","height(cm)":"89","RAW_FILE_NAME":"B-18.D"}
},
{
"Subject ID":"-",
"Sample ID":"A25",
"Factors":{"race":"White","sex":"F","category":"VUR"},
"Additional sample data":{"age_at_collection(years)":"4.824657534","weight(kg)":"17.4","height(cm)":"106","RAW_FILE_NAME":"A-25.D"}
},
{
"Subject ID":"-",
"Sample ID":"A26",
"Factors":{"race":"White","sex":"F","category":"No scarring"},
"Additional sample data":{"age_at_collection(years)":"4.073972603","weight(kg)":"15.9","height(cm)":"100","RAW_FILE_NAME":"A-26.D"}
},
{
"Subject ID":"-",
"Sample ID":"A27",
"Factors":{"race":"White","sex":"F","category":"No scarring"},
"Additional sample data":{"age_at_collection(years)":"4.375342466","weight(kg)":"18.3","height(cm)":"106","RAW_FILE_NAME":"A-27.D"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"Urine was collected from eligible children at clinic visits to a pediatric urologist","SAMPLE_TYPE":"Urine","COLLECTION_METHOD":"Clean catch or catheterized","COLLECTION_LOCATION":"Pediatric urology clinic","COLLECTION_FREQUENCY":"Once","STORAGE_CONDITIONS":"-80℃"},

"TREATMENT":{"TREATMENT_SUMMARY":"No treatments"},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"100 µL of freshly prepared 1 mg/mL urase solution was added to 100 µL of each of the urine samples then vortexed for 20 seconds and allowed to stand at -20 oC for 1 h. Next, 20 µL of 1 mg/mL of ribitol in water was added to each sample followed by addition of 1 mL of MeOH that was precooled to -20 ºC. The solution was again vortexed for 20 seconds and allowed to stand at -20 ºC for another 2 hours. The samples were centrifuged at 13000g for 15 minutes, and 1 ml of the supernatant from each sample was transferred to an autosampler vial and dried under gaseous nitrogen stream. Additionally, a pooled sample was prepared by combining 200 µL of supernatants from each sample and dried under nitrogen. Dried extracts were stored at -20 C until derivatization.","PROCESSING_STORAGE_CONDITIONS":"-20℃","EXTRACTION_METHOD":"For GCMS-polar analysis samples were extracted with water, containing 1 mg/ml ribitol, and 1 ml methanol.","EXTRACT_ENRICHMENT":"1 mL each of supernatant was collected from each sample for GCMS-polar analysis.","EXTRACT_STORAGE":"-20℃","SAMPLE_RESUSPENSION":"For GCMS analysis extracts dried under nitrogen flow and storred at -20C then resuspended in 25 μl of pyridine containing 15 mg/ml methoxyamine hydrochloride","SAMPLE_DERIVATIZATION":"GCMS samples were derivatized with 25 μl MSTFA (N-methyl-N-(trimethyl-silyl)trifluoroacetamide) + 1% TMCS (chlorotrimethylsilane)","SAMPLE_SPIKING":"Ribitol was used as internal standard for GCMS-polar analysis."},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_SUMMARY":"Gas chromatography integrated to mass spectrometer","CHROMATOGRAPHY_TYPE":"GC","INSTRUMENT_NAME":"Agilent 6890N","COLUMN_NAME":"DB-5MS (J&W Scientific) 60m","FLOW_RATE":"1mL/Min of Helium gas","COLUMN_TEMPERATURE":"80 0C for 2 minutes, then ramped at 5 0C /min to 315 ºC and held at 315 ºC for 12 minutes","COLUMN_PRESSURE":"variable","INJECTION_TEMPERATURE":"280C","INTERNAL_STANDARD":"Ribitol","RETENTION_TIME":"9 to 61 min","ANALYTICAL_TIME":"61 min","OVEN_TEMPERATURE":"80C to 315C","CHROMATOGRAPHY_COMMENTS":"1:1 split injection with 1uL injection volume"},

"ANALYSIS":{"ANALYSIS_TYPE":"MS","LABORATORY_NAME":"MU Metabolomics Center","OPERATOR_NAME":"Saurav Sarma","DETECTOR_TYPE":"Mass Spectrometer","DATA_FORMAT":".d"},

"MS":{"INSTRUMENT_NAME":"Agilent 5973","INSTRUMENT_TYPE":"Single quadrupole","MS_TYPE":"EI","ION_MODE":"POSITIVE","MS_COMMENTS":"Agilent Chem Station software used for data acquisition, Enhanced Data Analysis software used for converting data to .cdf file, AMDIS was used for peak deconvolution and NIST17 GCMS library was used for compound identification.","HELIUM_FLOW":"1mL/min","ION_SOURCE_TEMPERATURE":"230C","IONIZATION_ENERGY":"70ev","REAGENT_GAS":"Helium","SOURCE_TEMPERATURE":"230C","DATAFORMAT":".d","MS_RESULTS_FILE":"ST001649_AN002695_Results.txt UNITS:Intensity Has m/z:Yes Has RT:Yes RT units:Minutes"}

}