{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST000540","ANALYSIS_ID":"AN000820","VERSION":"1","CREATED_ON":"02-08-2024"},

"PROJECT":{"PROJECT_TITLE":"Kidney tissue metabolomic profiling of diabetic nephropathy in the steptozotocin induced type-1 diabetes mouse model.","PROJECT_SUMMARY":"Diabetic nephropathy (DN) is the leading cause of end stage renal disease, and is associated with high morbidity and mortality rates. The pathophysiology of DN includes both glomerular and tubulointerstitial damage. Meprins are metalloproteinases which are most abundantly expressed in the brush border membranes of proximal kidney tubules. Meprins are also expressed in leukocytes (monocytes and macrophages) and podocytes. Meprins have been implicated in the pathology of acute and chronic kidney injury. Single nucleotide polymorphisms (SNPs) in the meprin β gene were associated in human DN in the Pima Indians, suggesting a role for meprins in the pathophysiology of DN. The current study was done to determine the mechanisms by which meprins modulate the progression of DN in mice.","INSTITUTE":"North Carolina A&T State University","DEPARTMENT":"Department of Biology","LAST_NAME":"Ongeri","FIRST_NAME":"Elimelda Moige","ADDRESS":"1601 E Market Street, Greensboro, NC 27411","EMAIL":"eongeri@ncat.edu","PHONE":"336-285-2182","FUNDING_SOURCE":"NIH/NIGMS Grant # SC3102049; NIH Center Grant # U24DK097193; NIH/NCATS award # UL1TR001111; NIH/NIGMS Grant # K01GM109320","DOI":"http://dx.doi.org/10.21228/M80G60"},

"STUDY":{"STUDY_TITLE":"Kidney tissue metabolomic profiling of diabetic nephropathy in the steptozotocin induced type-1 diabetes mouse model.","STUDY_TYPE":"Metabolomics","STUDY_SUMMARY":"This metabolomics study evaluated kidney tissue from wild-type and meprin β knockout mice after induction of diabetes with streptozotocin or treatment with sodium citrate control to understand how these factors influence the metabotype.","INSTITUTE":"RTI International","DEPARTMENT":"Discovery-Science-Technology","LABORATORY":"NIH Eastern Regional Comphrehensive Metabolomics Resource Core at UNC Chapel Hill (ERCMRC)","LAST_NAME":"Sumner","FIRST_NAME":"Susan","ADDRESS":"3040 E Cornwallis Road, Research Triangle Park, NC 27709","EMAIL":"susan_sumner@unc.edu","PHONE":"704-250-5000","SUBMIT_DATE":"2017-01-20"},

"SUBJECT":{"SUBJECT_TYPE":"mice","SUBJECT_SPECIES":"Mus musculus","TAXONOMY_ID":"10090","GENOTYPE_STRAIN":"C57BL/6","GENDER":"Male","SPECIES_GROUP":"Mammal"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"-",
"Sample ID":"Equilibrium_6",
"Factors":{"Treatment":"-","Genotype":"-"},
"Additional sample data":{"Instrument Run Name (POS)":"MO_KT_Equil6_POS.raw","Instrument Run Name (NEG)":"MO_KT_Equil6_NEG.raw","Gender":"-"}
},
{
"Subject ID":"-",
"Sample ID":"Total Pool_1",
"Factors":{"Treatment":"-","Genotype":"-"},
"Additional sample data":{"Instrument Run Name (POS)":"MO_KT_Pool_1_POS.raw","Instrument Run Name (NEG)":"MO_KT_Pool_1_NEG.raw","Gender":"-"}
},
{
"Subject ID":"-",
"Sample ID":"Total Pool_2",
"Factors":{"Treatment":"-","Genotype":"-"},
"Additional sample data":{"Instrument Run Name (POS)":"MO_KT_Pool_2_POS.raw","Instrument Run Name (NEG)":"MO_KT_Pool_2_NEG.raw","Gender":"-"}
},
{
"Subject ID":"-",
"Sample ID":"Total Pool_3",
"Factors":{"Treatment":"-","Genotype":"-"},
"Additional sample data":{"Instrument Run Name (POS)":"MO_KT_Pool_3_POS.raw","Instrument Run Name (NEG)":"MO_KT_Pool_3_NEG.raw","Gender":"-"}
},
{
"Subject ID":"-",
"Sample ID":"Total Pool_4",
"Factors":{"Treatment":"-","Genotype":"-"},
"Additional sample data":{"Instrument Run Name (POS)":"MO_KT_Pool_4_POS_rerun.raw","Instrument Run Name (NEG)":"MO_KT_Pool_4_NEG.raw","Gender":"-"}
},
{
"Subject ID":"-",
"Sample ID":"383",
"Factors":{"Treatment":"NaC","Genotype":"Meprin bKO"},
"Additional sample data":{"Instrument Run Name (POS)":"MO_KT_KO_NaC_383 _POS.raw","Instrument Run Name (NEG)":"MO_KT_KO_NaC_383 _NEG.raw","Gender":"Male"}
},
{
"Subject ID":"-",
"Sample ID":"387",
"Factors":{"Treatment":"NaC","Genotype":"Meprin bKO"},
"Additional sample data":{"Instrument Run Name (POS)":"MO_KT_KO_NaC_387 _POS.raw","Instrument Run Name (NEG)":"-","Gender":"Male"}
},
{
"Subject ID":"-",
"Sample ID":"390",
"Factors":{"Treatment":"NaC","Genotype":"Meprin bKO"},
"Additional sample data":{"Instrument Run Name (POS)":"MO_KT_KO_NaC_390 _POS.raw","Instrument Run Name (NEG)":"MO_KT_KO_NaC_390 _NEG.raw","Gender":"Male"}
},
{
"Subject ID":"-",
"Sample ID":"391",
"Factors":{"Treatment":"NaC","Genotype":"Meprin bKO"},
"Additional sample data":{"Instrument Run Name (POS)":"MO_KT_KO_NaC_391 _POS.raw","Instrument Run Name (NEG)":"MO_KT_KO_NaC_391 _NEG.raw","Gender":"Male"}
},
{
"Subject ID":"-",
"Sample ID":"398",
"Factors":{"Treatment":"NaC","Genotype":"Meprin bKO"},
"Additional sample data":{"Instrument Run Name (POS)":"MO_KT_KO_NaC_398 _POS.raw","Instrument Run Name (NEG)":"-","Gender":"Male"}
},
{
"Subject ID":"-",
"Sample ID":"399",
"Factors":{"Treatment":"NaC","Genotype":"Meprin bKO"},
"Additional sample data":{"Instrument Run Name (POS)":"MO_KT_KO_NaC_399 _POS.raw","Instrument Run Name (NEG)":"MO_KT_KO_NaC_399 _NEG.raw","Gender":"Male"}
},
{
"Subject ID":"-",
"Sample ID":"519",
"Factors":{"Treatment":"NaC","Genotype":"wild-type"},
"Additional sample data":{"Instrument Run Name (POS)":"MO_KT_WT_NaC_519 _POS.raw","Instrument Run Name (NEG)":"MO_KT_WT_NaC_519 _NEG.raw","Gender":"Male"}
},
{
"Subject ID":"-",
"Sample ID":"520",
"Factors":{"Treatment":"NaC","Genotype":"wild-type"},
"Additional sample data":{"Instrument Run Name (POS)":"MO_KT_WT_NaC_520 _POS.raw","Instrument Run Name (NEG)":"MO_KT_WT_NaC_520 _NEG.raw","Gender":"Male"}
},
{
"Subject ID":"-",
"Sample ID":"521",
"Factors":{"Treatment":"NaC","Genotype":"wild-type"},
"Additional sample data":{"Instrument Run Name (POS)":"-","Instrument Run Name (NEG)":"MO_KT_WT_NaC_521 _NEG.raw","Gender":"Male"}
},
{
"Subject ID":"-",
"Sample ID":"522",
"Factors":{"Treatment":"NaC","Genotype":"wild-type"},
"Additional sample data":{"Instrument Run Name (POS)":"MO_KT_WT_NaC_522 _POS.raw","Instrument Run Name (NEG)":"MO_KT_WT_NaC_522 _NEG.raw","Gender":"Male"}
},
{
"Subject ID":"-",
"Sample ID":"523",
"Factors":{"Treatment":"NaC","Genotype":"wild-type"},
"Additional sample data":{"Instrument Run Name (POS)":"MO_KT_WT_NaC_523 _POS.raw","Instrument Run Name (NEG)":"MO_KT_WT_NaC_523 _NEG.raw","Gender":"Male"}
},
{
"Subject ID":"-",
"Sample ID":"395",
"Factors":{"Treatment":"STZ","Genotype":"Meprin bKO"},
"Additional sample data":{"Instrument Run Name (POS)":"MO_KT_KO_STZ_395 _POS.raw","Instrument Run Name (NEG)":"MO_KT_KO_STZ_395 _NEG.raw","Gender":"Male"}
},
{
"Subject ID":"-",
"Sample ID":"396",
"Factors":{"Treatment":"STZ","Genotype":"Meprin bKO"},
"Additional sample data":{"Instrument Run Name (POS)":"MO_KT_KO_STZ_396 _POS.raw","Instrument Run Name (NEG)":"MO_KT_KO_STZ_396 _NEG.raw","Gender":"Male"}
},
{
"Subject ID":"-",
"Sample ID":"397",
"Factors":{"Treatment":"STZ","Genotype":"Meprin bKO"},
"Additional sample data":{"Instrument Run Name (POS)":"MO_KT_KO_STZ_397 _POS.raw","Instrument Run Name (NEG)":"MO_KT_KO_STZ_397 _NEG.raw","Gender":"Male"}
},
{
"Subject ID":"-",
"Sample ID":"400",
"Factors":{"Treatment":"STZ","Genotype":"Meprin bKO"},
"Additional sample data":{"Instrument Run Name (POS)":"MO_KT_KO_STZ_400 _POS.raw","Instrument Run Name (NEG)":"MO_KT_KO_STZ_400 _NEG.raw","Gender":"Male"}
},
{
"Subject ID":"-",
"Sample ID":"514",
"Factors":{"Treatment":"STZ","Genotype":"Meprin bKO"},
"Additional sample data":{"Instrument Run Name (POS)":"MO_KT_KO_STZ_514 _POS.raw","Instrument Run Name (NEG)":"MO_KT_KO_STZ_514 _NEG.raw","Gender":"Male"}
},
{
"Subject ID":"-",
"Sample ID":"515",
"Factors":{"Treatment":"STZ","Genotype":"Meprin bKO"},
"Additional sample data":{"Instrument Run Name (POS)":"MO_KT_KO_STZ_515 _POS.raw","Instrument Run Name (NEG)":"MO_KT_KO_STZ_515 _NEG.raw","Gender":"Male"}
},
{
"Subject ID":"-",
"Sample ID":"516",
"Factors":{"Treatment":"STZ","Genotype":"Meprin bKO"},
"Additional sample data":{"Instrument Run Name (POS)":"MO_KT_KO_STZ_516 _POS.raw","Instrument Run Name (NEG)":"MO_KT_KO_STZ_516 _NEG.raw","Gender":"Male"}
},
{
"Subject ID":"-",
"Sample ID":"518",
"Factors":{"Treatment":"STZ","Genotype":"Meprin bKO"},
"Additional sample data":{"Instrument Run Name (POS)":"MO_KT_KO_STZ_518 _POS.raw","Instrument Run Name (NEG)":"MO_KT_KO_STZ_518 _NEG.raw","Gender":"Male"}
},
{
"Subject ID":"-",
"Sample ID":"525",
"Factors":{"Treatment":"STZ","Genotype":"wild-type"},
"Additional sample data":{"Instrument Run Name (POS)":"MO_KT_WT_STZ_525 _POS.raw","Instrument Run Name (NEG)":"MO_KT_WT_STZ_525 _NEG.raw","Gender":"Male"}
},
{
"Subject ID":"-",
"Sample ID":"526",
"Factors":{"Treatment":"STZ","Genotype":"wild-type"},
"Additional sample data":{"Instrument Run Name (POS)":"MO_KT_WT_STZ_526 _POS.raw","Instrument Run Name (NEG)":"MO_KT_WT_STZ_526 _NEG.raw","Gender":"Male"}
},
{
"Subject ID":"-",
"Sample ID":"528",
"Factors":{"Treatment":"STZ","Genotype":"wild-type"},
"Additional sample data":{"Instrument Run Name (POS)":"MO_KT_WT_STZ_528 _POS.raw","Instrument Run Name (NEG)":"MO_KT_WT_STZ_528 _NEG.raw","Gender":"Male"}
},
{
"Subject ID":"-",
"Sample ID":"529",
"Factors":{"Treatment":"STZ","Genotype":"wild-type"},
"Additional sample data":{"Instrument Run Name (POS)":"MO_KT_WT_STZ_529 _POS.raw","Instrument Run Name (NEG)":"MO_KT_WT_STZ_529 _NEG.raw","Gender":"Male"}
},
{
"Subject ID":"-",
"Sample ID":"530",
"Factors":{"Treatment":"STZ","Genotype":"wild-type"},
"Additional sample data":{"Instrument Run Name (POS)":"MO_KT_WT_STZ_530 _POS.raw","Instrument Run Name (NEG)":"MO_KT_WT_STZ_530 _NEG.raw","Gender":"Male"}
},
{
"Subject ID":"-",
"Sample ID":"531",
"Factors":{"Treatment":"STZ","Genotype":"wild-type"},
"Additional sample data":{"Instrument Run Name (POS)":"MO_KT_WT_STZ_531 _POS.raw","Instrument Run Name (NEG)":"MO_KT_WT_STZ_531 _NEG.raw","Gender":"Male"}
},
{
"Subject ID":"-",
"Sample ID":"532",
"Factors":{"Treatment":"STZ","Genotype":"wild-type"},
"Additional sample data":{"Instrument Run Name (POS)":"MO_KT_WT_STZ_532 _POS.raw","Instrument Run Name (NEG)":"MO_KT_WT_STZ_532 _NEG.raw","Gender":"Male"}
},
{
"Subject ID":"-",
"Sample ID":"533",
"Factors":{"Treatment":"STZ","Genotype":"wild-type"},
"Additional sample data":{"Instrument Run Name (POS)":"MO_KT_WT_STZ_533 _POS.raw","Instrument Run Name (NEG)":"MO_KT_WT_STZ_533 _NEG.raw","Gender":"Male"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"Kidneys were harvested at 8-weeks post STZ-injection. The mice were sacrificed by CO2 asphyxiation. The kidneys were excised, decapsulated and individually weighed, snap-frozen in liquid nitrogen, and stored at -80oC until used.","SAMPLE_TYPE":"Kidney Tissue","STORAGE_CONDITIONS":"-80C"},

"TREATMENT":{"TREATMENT_SUMMARY":"Type 1 diabetes was induced at age 8 weeks. The mice were fasted for 6 hours prior to being injected with low dose STZ (50 mg/kg body weight) in sodium citrate buffer (10 mmol/L, pH 4.5) daily for 5 days following the protocols described by Tesch and Allen and recommended by the Animal Models of Diabetic Complications Consortium (AMDCC; amdcc.org)1. Control mice were injected with equivalent volumes of the sodium citrate buffer. Diabetes was confirmed by measuring fasting blood glucose levels using a standard glucose meter at 10 days post-STZ injection. Mice with a fasting glucose level ≥280 mg/dL were considered diabetic. STZ-injected mice with a fasting blood glucose of <280 mg/dL (15mmol/L) were culled and eliminated from the study.","TREATMENT_COMPOUND":"streptozotocin","TREATMENT_DOSE":"50 mg/kg body weight","TREATMENT_DOSEDURATION":"daily; 5 days","TREATMENT_VEHICLE":"sodium citrate","ANIMAL_ENDP_TISSUE_COLL_LIST":"plasma, urine, kidney tissue"},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"Frozen kidney tissue samples on dry ice were transferred to pre-chilled, pre-labeled tubes, and their weights recorded. For every 1 mg of tissue sample, 2 µL of 50:50 Acetonitrile:Water was added to the tube. Ceramic beads (2.3 mm; ~15-20 prewashed & dried) were added to the tubes, and the samples were homogenized on the MagNA Lyser system using a 30 s pulse at 4,000 rpm. The samples were centrifuged at room temperature at 16,000 rcf for 4 min. An aliquot of the supernatant was transferred to pre-labeled 2.0 mL low protein-binding microcentrifuge tube to make the individual study sample (40 µL). Another aliquot of supernatant (18 µL) was combined with those from all other kidney tissue samples in a 1.5 mL low protein-binding microcentrifuge tube to make the total pool quality control sample. The total pool quality control sample was aliquoted (40 µL) to make 4 Total Pool Samples and 4 Column Equilibration samples. 132 µL of the total pool quality control sample was added to the total study sample pool to make a pool of kidney, urine, and plasma samples. The total study pool sample was used to prepare 9 Total Study Samples (40 µL) to aid in alignment of the three studies. Of these, 3 total study samples were included in the kidney tissue analysis. Acetonitrile containing the internal standard Tryptophan-d5 (460 µL; 0.0125 mg/ml) was added to all samples, and samples were vortexed on a multiple tube vortexer for 2 min at 5000 rpm followed by centrifugation at 16,000 rcf for 4 min. The supernatants (420 µL) were transferred into new, pre-labeled 2.0 mL low protein-binding microcentrifuge tubes and capped with disposable rubber stoppers. Samples were placed at -80 °C for 1.5 h and lyophilized for 18 h. Acetonitrile:Water (150 µL; 95:5) was added to each tube and vortex mixed for 10 min at 5000 rpm, followed by centrifugation at room temperature at 16,000 rcf for 4 min. The supernatants were transferred to pre-labeled autosampler vials and 3 µL was injected into SYNAPT G2 Si."},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_SUMMARY":"Hydrophilic Interaction Liquid Chromatography (HILIC) Gradient Seperation","INSTRUMENT_NAME":"Waters Acquity I-Class","COLUMN_NAME":"Waters Acquity BEH Amide (150 x 2.1mm,1.7um)","CHROMATOGRAPHY_TYPE":"HILIC"},

"ANALYSIS":{"ANALYSIS_TYPE":"MS"},

"MS":{"INSTRUMENT_NAME":"Waters Synapt G2 Si QTOF","INSTRUMENT_TYPE":"QTOF","MS_TYPE":"ESI","ION_MODE":"POSITIVE"}

}