{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST001303","ANALYSIS_ID":"AN002170","VERSION":"1","CREATED_ON":"January 9, 2020, 1:15 pm"},

"PROJECT":{"PROJECT_TITLE":"TGFβ3 heterozygous mice","PROJECT_TYPE":"Mice nephropathy in lipotoxic model","PROJECT_SUMMARY":"Transforming growth factor β (TGFβ) family comprises the main player in the development of fibrosis including three isoforms: TGFβ1, TGFβ2 and TGFβ3. TGFβ3 may play an antifibrotic role at the renal level, counteracting the role of TGFβ1, using a mouse model heterozygous for the TGFβ3 gene (TGFβ3+/-). Partial deletion of TGFβ3 causes in the mice albuminuria, loss of glomerular filtration rate, accelerated fibrosis, epithelial-to-mesenchymal transition and increment of glomerular basement membrane thickening.","INSTITUTE":"University Rey Juan Carlos","DEPARTMENT":"Basics Science of Health","LAST_NAME":"Lanzon","FIRST_NAME":"Borja","ADDRESS":"Avenida de Atenas S/N, Alcorcón, Madrid, 28922, Spain","EMAIL":"borja.lanzon@urjc.es","PHONE":"663692554"},

"STUDY":{"STUDY_TITLE":"TGF-Beta 3 heterozygous mice","STUDY_TYPE":"Mice nephropathy in lipotoxic model","STUDY_SUMMARY":"Transforming growth factor β (TGFβ) family comprises the main player in the development of fibrosis including three isoforms: TGFβ1, TGFβ2 and TGFβ3. TGFβ3 may play an antifibrotic role at the renal level, counteracting the role of TGFβ1, using a mouse model heterozygous for the TGFβ3 gene (TGFβ3+/-). Partial deletion of TGFβ3 causes in the mice albuminuria, loss of glomerular filtration rate, accelerated fibrosis, epithelial-to-mesenchymal transition and increment of glomerular basement membrane thickening.","INSTITUTE":"University Rey Juan Carlos","DEPARTMENT":"Basics Science of Health","LAST_NAME":"Lanzon","FIRST_NAME":"Borja","ADDRESS":"Avenida de Atenas S/N","EMAIL":"borja.lanzon@urjc.es","PHONE":"663692554","NUM_GROUPS":"2","TOTAL_SUBJECTS":"14","NUM_MALES":"14"},

"SUBJECT":{"SUBJECT_TYPE":"Mammal","SUBJECT_SPECIES":"Mus musculus","TAXONOMY_ID":"10090","GENOTYPE_STRAIN":"c57bl6","AGE_OR_AGE_RANGE":"16 weeks","GENDER":"Male"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"-",
"Sample ID":"269 HZCD",
"Factors":{"Genotype":"HZCD"},
"Additional sample data":{"RAW_FILE_NAME":"HZ-CD 269"}
},
{
"Subject ID":"-",
"Sample ID":"119 HZCD",
"Factors":{"Genotype":"HZCD"},
"Additional sample data":{"RAW_FILE_NAME":"HZ-CD 119"}
},
{
"Subject ID":"-",
"Sample ID":"267 HZCD",
"Factors":{"Genotype":"HZCD"},
"Additional sample data":{"RAW_FILE_NAME":"HZ-CD 267"}
},
{
"Subject ID":"-",
"Sample ID":"130 HZCD",
"Factors":{"Genotype":"HZCD"},
"Additional sample data":{"RAW_FILE_NAME":"HZ-CD 130"}
},
{
"Subject ID":"-",
"Sample ID":"127 HZCD",
"Factors":{"Genotype":"HZCD"},
"Additional sample data":{"RAW_FILE_NAME":"HZ-CD 127"}
},
{
"Subject ID":"-",
"Sample ID":"98 HZCD",
"Factors":{"Genotype":"HZCD"},
"Additional sample data":{"RAW_FILE_NAME":"HZ-CD 98"}
},
{
"Subject ID":"-",
"Sample ID":"25 HZCD",
"Factors":{"Genotype":"HZCD"},
"Additional sample data":{"RAW_FILE_NAME":"HZ-CD 25"}
},
{
"Subject ID":"-",
"Sample ID":"132 WTCD",
"Factors":{"Genotype":"WTCD"},
"Additional sample data":{"RAW_FILE_NAME":"WT-CD 132"}
},
{
"Subject ID":"-",
"Sample ID":"251 WTCD",
"Factors":{"Genotype":"WTCD"},
"Additional sample data":{"RAW_FILE_NAME":"WT-CD 251"}
},
{
"Subject ID":"-",
"Sample ID":"120 WTCD",
"Factors":{"Genotype":"WTCD"},
"Additional sample data":{"RAW_FILE_NAME":"WT-CD 120"}
},
{
"Subject ID":"-",
"Sample ID":"79 WTCD",
"Factors":{"Genotype":"WTCD"},
"Additional sample data":{"RAW_FILE_NAME":"WT-CD 79"}
},
{
"Subject ID":"-",
"Sample ID":"129 WTCD",
"Factors":{"Genotype":"WTCD"},
"Additional sample data":{"RAW_FILE_NAME":"WT-CD 129"}
},
{
"Subject ID":"-",
"Sample ID":"128 WTCD",
"Factors":{"Genotype":"WTCD"},
"Additional sample data":{"RAW_FILE_NAME":"WT-CD 128"}
},
{
"Subject ID":"-",
"Sample ID":"92 WTCD",
"Factors":{"Genotype":"WTCD"},
"Additional sample data":{"RAW_FILE_NAME":"WT-CD 92"}
},
{
"Subject ID":"-",
"Sample ID":"QC1",
"Factors":{"Genotype":"QC"},
"Additional sample data":{"RAW_FILE_NAME":"QC1"}
},
{
"Subject ID":"-",
"Sample ID":"QC2",
"Factors":{"Genotype":"QC"},
"Additional sample data":{"RAW_FILE_NAME":"QC2"}
},
{
"Subject ID":"-",
"Sample ID":"QC3",
"Factors":{"Genotype":"QC"},
"Additional sample data":{"RAW_FILE_NAME":"QC3"}
},
{
"Subject ID":"-",
"Sample ID":"QC4",
"Factors":{"Genotype":"QC"},
"Additional sample data":{"RAW_FILE_NAME":"QC4"}
},
{
"Subject ID":"-",
"Sample ID":"QC5",
"Factors":{"Genotype":"QC"},
"Additional sample data":{"RAW_FILE_NAME":"QC5"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"Kidney samples were powdered with mortar and pestle. Method used for extraction was previously validated for tissue","SAMPLE_TYPE":"Kidney","STORAGE_CONDITIONS":"-80℃"},

"TREATMENT":{"TREATMENT_SUMMARY":"Kidney homogenate was prepared by adding cold (−20 °C) methanol/water (1:1, v/v), (1:10 tissue/solvent). Tissue disruption was achieved with Tissue- Lyser LT homogenizer (Qiagen, Germany) for metabolite extraction."},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"100 μL of kidney tissue homogenate was vortex-mixed with 320 μL of methanol for 2 min, followed by the addition of 80 μL of MTBE for the extraction of nonpolar compounds. Then, vials were rapidly capped and placed on a shaker for 1 h at room temperature. The extracted samples were centrifuged at 4000g for 20 min at 20 °C. For GC−MS analysis, 300 μL of supernatant was evaporated to dryness (SpeedVac Concentrator System, Thermo Fisher Scientific, Waltham, MA). Methoxymation was then performed with 20 μL of O-methoxyamine hydrochloride (15 mg/mL in pyridine) and vigorously vortex-mixed for 5 min. Vials were then incubated in darkness at room temperature for 16 h. For silylation, 20 μL of BSTFA/TMCS (99:1) was added and vortex-mixed for 5 min, and capped vials were placed in the oven at 70 °C for 1 h. Finally, 100 μL of heptane containing tricosane (20 ppm) as internal standard (IS) was added to each vial prior to injection. For LC−MS analysis, 90 μL of supernatant was transferred to an ultra-high-performance liquid chromatography−mass spectrometry.","PROCESSING_STORAGE_CONDITIONS":"On ice","EXTRACT_STORAGE":"-80℃"},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_SUMMARY":"LC-MS (-)","CHROMATOGRAPHY_TYPE":"Reversed phase","INSTRUMENT_NAME":"Agilent 1290 Infinity II","COLUMN_NAME":"Poroshell 120 EC-C8 (100 x 2.1mm, 2.5um)"},

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

"MS":{"INSTRUMENT_NAME":"Agilent 6545","INSTRUMENT_TYPE":"QTOF","MS_TYPE":"ESI","ION_MODE":"NEGATIVE","MS_COMMENTS":"A UHPLC system (1290 Infinity UHPLC system, Agilent Technologies, Waldbronn, Germany), consisting of two degassers, two binary pumps, and a thermostated autosampler (maintained at 4°C) coupled with 6545 QTOF MS detector, was used in positive and negative ESI modes. In brief, 1 μL of each sample was injected into a reverse-phase Zorbax Eclipse Plus C8 column, 2.1 × 150 mm; 1.8 μm (Agilent Technologies) thermostated at 60°C. The gradient used for the analysis consisted of a mobile phase A (0.1% formic acid in Milli-Q water) and mobile phase B (0.1% formic acid in methanol:isopropanol, 85:15) pumped at 0.5 mL/min. The chromatography gradient started at 82% phase B, increasing to 90% B in 17 min. The gradient then increased to 100% B by minute 18 and was maintained for 2 minutes until 20 min. The starting condition was returned to by 21.5 min, followed by an 8.5 min reequilibration time, taking the total run time to 30 min. Data were collected in full scan mode from 100 to 1000 m/z for the negative modes, with a scan rate of 1.02 scans/s. The capillary voltage was set to 3000 V; the drying gas flow rate was 12 L/min at 290°C and gas nebulizer 45 psi, fragmentor voltage 175 V, and octopole radio frequency voltage (OCT RF Vpp) 750 V. Two reference masses were used over the course of the whole analysis: m/z 112.9856 (proton-abstracted TFA anion) and m/z 966.0007 (formate adduct of HP921) for the negative mode. These masses were continuously infused into the system to provide constant mass correction. Samples were randomly analyzed throughout the run.","MS_RESULTS_FILE":"ST001303_AN002170_Results.txt UNITS:Area Has m/z:Neutral masses Has RT:Yes RT units:Minutes"}

}