{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST003043","ANALYSIS_ID":"AN004992","VERSION":"1","CREATED_ON":"01-19-2024"},

"PROJECT":{"PROJECT_TITLE":"Retinoid levels measurement in kidney and serum","PROJECT_TYPE":"MS analysis","PROJECT_SUMMARY":"Chronic kidney disease (CKD) is characterized by a gradual loss of kidney function and affects ca. 13.4% of the global population. Progressive tubulointerstitial fibrosis, driven in part by proximal tubule (PT) damage, is a hallmark of late stages of CKD and contributes to the development of kidney failure, for which there are limited treatment options. Normal kidney development requires signaling by vitamin A (retinol), which is metabolized to retinoic acid (RA), an endogenous agonist for the retinoic acid receptors (RAR alpha, beta, gamma). RARalpha levels are decreased in a mouse model of diabetic nephropathy (DN) and restored with RA administration; additionally, RA treatment reduces fibrosis. We developed a mouse model in which a spatiotemporal (tamoxifen-inducible) deletion of RARalpha in kidney PT cells of adult mice causes mitochondrial dysfunction, massive PT injury, and apoptosis without the use of additional nephrotoxic substances. Long-term effects (3-4.5 months) of RARalpha deletion include increased PT secretion of transforming growth factor beta (TGF-beta1), inflammation, interstitial fibrosis, and decreased kidney function, all of which are major features of human CKD. Therefore, RARalpha’s actions in proximal tubules (PTs) are crucial for PT homeostasis, and loss of RARalpha causes injury and a key CKD phenotype.","INSTITUTE":"Weill Cornell Medicine","LAST_NAME":"Tang","FIRST_NAME":"Xiao-Han","ADDRESS":"1300 Yates Avenue, New York, NY 10065","EMAIL":"xit2001@med.cornell.edu","PHONE":"3478327329","PUBLICATIONS":"DiKun KM et al, RETINOIC ACID RECEPTOR a ACTIVITY IN PROXIMAL TUBULES PREVENTS KIDNEY INJURY AND FIBROSIS. PNAS, 2024.","DOI":"http://dx.doi.org/10.21228/M8WQ6G"},

"STUDY":{"STUDY_TITLE":"Retinoic acid receptor alpha activity in proximal tubules prevents kidney injury and fibrosis","STUDY_SUMMARY":"Retinoid levels of all-trans-retinol, retinoic acid, and retinyl palmitate were measured in the kidney and serum of GCERRARaD (kidney proximal tubule RARalpha knockout mice) females 3 days or 3 months post-tamoxifen (n=5/group) and age-matched Wild Type females (n=4).","INSTITUTE":"Weill Cornell Medicine","LAST_NAME":"Tang","FIRST_NAME":"Xiao-Han","ADDRESS":"1300 York Ave, New York, NY10065","EMAIL":"xit2001@med.cornell.edu","PHONE":"3478327329","SUBMIT_DATE":"2024-01-14"},

"SUBJECT":{"SUBJECT_TYPE":"Mammal","SUBJECT_SPECIES":"Mus musculus","TAXONOMY_ID":"10090","GENDER":"Female"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"C13 T1",
"Sample ID":"Kidney3DM1negative",
"Factors":{"Genotype":"Mutant","Treatment":"tamoxifen, 3day"},
"Additional sample data":{"Batch":"1a","Ion mode":"negative","RAW_FILE_NAME":"K3DM1.mzML"}
},
{
"Subject ID":"C13 T2",
"Sample ID":"Kidney3DM2negative",
"Factors":{"Genotype":"Mutant","Treatment":"tamoxifen, 3day"},
"Additional sample data":{"Batch":"1a","Ion mode":"negative","RAW_FILE_NAME":"K3DM2.mzML"}
},
{
"Subject ID":"C13 T3",
"Sample ID":"Kidney3DM3negative",
"Factors":{"Genotype":"Mutant","Treatment":"tamoxifen, 3day"},
"Additional sample data":{"Batch":"1a","Ion mode":"negative","RAW_FILE_NAME":"K3DM3.mzML"}
},
{
"Subject ID":"C13 T4",
"Sample ID":"Kidney3DM4negative",
"Factors":{"Genotype":"Mutant","Treatment":"tamoxifen, 3day"},
"Additional sample data":{"Batch":"1a","Ion mode":"negative","RAW_FILE_NAME":"K3DM4.mzML"}
},
{
"Subject ID":"C13 T5",
"Sample ID":"Kidney3DM5negative",
"Factors":{"Genotype":"Mutant","Treatment":"tamoxifen, 3day"},
"Additional sample data":{"Batch":"1a","Ion mode":"negative","RAW_FILE_NAME":"K3DM5.mzML"}
},
{
"Subject ID":"C13 T1",
"Sample ID":"Serum3DMN1negative",
"Factors":{"Genotype":"Mutant","Treatment":"tamoxifen, 3day"},
"Additional sample data":{"Batch":"1a","Ion mode":"negative","RAW_FILE_NAME":"S3DMN1.mzML"}
},
{
"Subject ID":"C13 T2",
"Sample ID":"Serum3DMN2negative",
"Factors":{"Genotype":"Mutant","Treatment":"tamoxifen, 3day"},
"Additional sample data":{"Batch":"1a","Ion mode":"negative","RAW_FILE_NAME":"S3DMN2.mzML"}
},
{
"Subject ID":"C13 T3",
"Sample ID":"Serum3DMN3neagtive",
"Factors":{"Genotype":"Mutant","Treatment":"tamoxifen, 3day"},
"Additional sample data":{"Batch":"1a","Ion mode":"negative","RAW_FILE_NAME":"S3DMN3.mzML"}
},
{
"Subject ID":"C13 T4",
"Sample ID":"Serum3DMN4negative",
"Factors":{"Genotype":"Mutant","Treatment":"tamoxifen, 3day"},
"Additional sample data":{"Batch":"1a","Ion mode":"negative","RAW_FILE_NAME":"S3DMN4.mzML"}
},
{
"Subject ID":"C13 T5",
"Sample ID":"Serum3DMN5negative",
"Factors":{"Genotype":"Mutant","Treatment":"tamoxifen, 3day"},
"Additional sample data":{"Batch":"1a","Ion mode":"negative","RAW_FILE_NAME":"S3DMN5.mzML"}
},
{
"Subject ID":"C13 T1",
"Sample ID":"Serum3DMP1positive",
"Factors":{"Genotype":"Mutant","Treatment":"tamoxifen, 3day"},
"Additional sample data":{"Batch":"1a","Ion mode":"positive","RAW_FILE_NAME":"S3DMP1.mzML"}
},
{
"Subject ID":"C13 T2",
"Sample ID":"Serum3DMP2positive",
"Factors":{"Genotype":"Mutant","Treatment":"tamoxifen, 3day"},
"Additional sample data":{"Batch":"1a","Ion mode":"positive","RAW_FILE_NAME":"S3DMP2.mzML"}
},
{
"Subject ID":"C13 T3",
"Sample ID":"Serum3DMP3positive",
"Factors":{"Genotype":"Mutant","Treatment":"tamoxifen, 3day"},
"Additional sample data":{"Batch":"1a","Ion mode":"positive","RAW_FILE_NAME":"S3DMP3.mzML"}
},
{
"Subject ID":"C13 T4",
"Sample ID":"Serum3DMP4positive",
"Factors":{"Genotype":"Mutant","Treatment":"tamoxifen, 3day"},
"Additional sample data":{"Batch":"1a","Ion mode":"positive","RAW_FILE_NAME":"S3DMP4.mzML"}
},
{
"Subject ID":"C13 T5",
"Sample ID":"Serum3DMP5positive",
"Factors":{"Genotype":"Mutant","Treatment":"tamoxifen, 3day"},
"Additional sample data":{"Batch":"1a","Ion mode":"positive","RAW_FILE_NAME":"S3DMP5.mzML"}
},
{
"Subject ID":"C4 T1",
"Sample ID":"Kidney3MM1negative",
"Factors":{"Genotype":"Mutant","Treatment":"tamoxifen, 3month"},
"Additional sample data":{"Batch":"1a","Ion mode":"negative","RAW_FILE_NAME":"K3MM1.mzML"}
},
{
"Subject ID":"C5 T1",
"Sample ID":"Kidney3MM2negative",
"Factors":{"Genotype":"Mutant","Treatment":"tamoxifen, 3month"},
"Additional sample data":{"Batch":"1a","Ion mode":"negative","RAW_FILE_NAME":"K3MM2.mzML"}
},
{
"Subject ID":"C5 T2",
"Sample ID":"Kidney3MM3negative",
"Factors":{"Genotype":"Mutant","Treatment":"tamoxifen, 3month"},
"Additional sample data":{"Batch":"1a","Ion mode":"negative","RAW_FILE_NAME":"K3MM3.mzML"}
},
{
"Subject ID":"C6 T1",
"Sample ID":"Kidney3MM4negative",
"Factors":{"Genotype":"Mutant","Treatment":"tamoxifen, 3month"},
"Additional sample data":{"Batch":"1a","Ion mode":"negative","RAW_FILE_NAME":"K3MM4.mzML"}
},
{
"Subject ID":"C6 T2",
"Sample ID":"Kidney3MM5negative",
"Factors":{"Genotype":"Mutant","Treatment":"tamoxifen, 3month"},
"Additional sample data":{"Batch":"1a","Ion mode":"negative","RAW_FILE_NAME":"K3MM5.mzML"}
},
{
"Subject ID":"C4 T1",
"Sample ID":"Serum3MMN1negative",
"Factors":{"Genotype":"Mutant","Treatment":"tamoxifen, 3month"},
"Additional sample data":{"Batch":"1a","Ion mode":"negative","RAW_FILE_NAME":"S3MMN1.mzML"}
},
{
"Subject ID":"C5 T1",
"Sample ID":"Serum3MMN2negative",
"Factors":{"Genotype":"Mutant","Treatment":"tamoxifen, 3month"},
"Additional sample data":{"Batch":"1a","Ion mode":"negative","RAW_FILE_NAME":"S3MMN2.mzML"}
},
{
"Subject ID":"C5 T2",
"Sample ID":"Serum3MMN3negative",
"Factors":{"Genotype":"Mutant","Treatment":"tamoxifen, 3month"},
"Additional sample data":{"Batch":"1a","Ion mode":"negative","RAW_FILE_NAME":"S3MMN3.mzML"}
},
{
"Subject ID":"C6 T1",
"Sample ID":"Serum3MMN4negative",
"Factors":{"Genotype":"Mutant","Treatment":"tamoxifen, 3month"},
"Additional sample data":{"Batch":"1a","Ion mode":"negative","RAW_FILE_NAME":"S3MMN4.mzML"}
},
{
"Subject ID":"C6 T2",
"Sample ID":"Serum3MMN5negative",
"Factors":{"Genotype":"Mutant","Treatment":"tamoxifen, 3month"},
"Additional sample data":{"Batch":"1a","Ion mode":"negative","RAW_FILE_NAME":"S3MMN5.mzML"}
},
{
"Subject ID":"C4 T1",
"Sample ID":"Serum3MMP1positive",
"Factors":{"Genotype":"Mutant","Treatment":"tamoxifen, 3month"},
"Additional sample data":{"Batch":"1a","Ion mode":"positive","RAW_FILE_NAME":"S3MMP1.mzML"}
},
{
"Subject ID":"C5 T1",
"Sample ID":"Serum3MMP2positive",
"Factors":{"Genotype":"Mutant","Treatment":"tamoxifen, 3month"},
"Additional sample data":{"Batch":"1a","Ion mode":"positive","RAW_FILE_NAME":"S3MMP2.mzML"}
},
{
"Subject ID":"C5 T2",
"Sample ID":"Serum3MMP3positive",
"Factors":{"Genotype":"Mutant","Treatment":"tamoxifen, 3month"},
"Additional sample data":{"Batch":"1a","Ion mode":"positive","RAW_FILE_NAME":"S3MMP3.mzML"}
},
{
"Subject ID":"C6 T1",
"Sample ID":"Serum3MMP4positive",
"Factors":{"Genotype":"Mutant","Treatment":"tamoxifen, 3month"},
"Additional sample data":{"Batch":"1a","Ion mode":"positive","RAW_FILE_NAME":"S3MMP4.mzML"}
},
{
"Subject ID":"C6 T2",
"Sample ID":"Serum3MMP5positive",
"Factors":{"Genotype":"Mutant","Treatment":"tamoxifen, 3month"},
"Additional sample data":{"Batch":"1a","Ion mode":"positive","RAW_FILE_NAME":"S3MMP5.mzML"}
},
{
"Subject ID":"WT22",
"Sample ID":"Kidney3DW1negative",
"Factors":{"Genotype":"Wild_Type","Treatment":"tamoxifen, 3day"},
"Additional sample data":{"Batch":"1a","Ion mode":"negative","RAW_FILE_NAME":"K3DW1.mzML"}
},
{
"Subject ID":"WT23",
"Sample ID":"Kidney3DW2negative",
"Factors":{"Genotype":"Wild_Type","Treatment":"tamoxifen, 3day"},
"Additional sample data":{"Batch":"1a","Ion mode":"negative","RAW_FILE_NAME":"K3DW2.mzML"}
},
{
"Subject ID":"WT24",
"Sample ID":"Kidney3DW3negative",
"Factors":{"Genotype":"Wild_Type","Treatment":"tamoxifen, 3day"},
"Additional sample data":{"Batch":"1a","Ion mode":"negative","RAW_FILE_NAME":"K3DW3.mzML"}
},
{
"Subject ID":"WT25",
"Sample ID":"Kidney3DW4negative",
"Factors":{"Genotype":"Wild_Type","Treatment":"tamoxifen, 3day"},
"Additional sample data":{"Batch":"1a","Ion mode":"negative","RAW_FILE_NAME":"K3DW4.mzML"}
},
{
"Subject ID":"WT22",
"Sample ID":"Serum3DWN1negative",
"Factors":{"Genotype":"Wild_Type","Treatment":"tamoxifen, 3day"},
"Additional sample data":{"Batch":"1a","Ion mode":"negative","RAW_FILE_NAME":"S3DWN1.mzML"}
},
{
"Subject ID":"WT23",
"Sample ID":"Serum3DWN2negative",
"Factors":{"Genotype":"Wild_Type","Treatment":"tamoxifen, 3day"},
"Additional sample data":{"Batch":"1a","Ion mode":"negative","RAW_FILE_NAME":"S3DWN2.mzML"}
},
{
"Subject ID":"WT24",
"Sample ID":"Serum3DWN3negative",
"Factors":{"Genotype":"Wild_Type","Treatment":"tamoxifen, 3day"},
"Additional sample data":{"Batch":"1a","Ion mode":"negative","RAW_FILE_NAME":"S3DWN3.mzML"}
},
{
"Subject ID":"WT25",
"Sample ID":"Serum3DWN4negative",
"Factors":{"Genotype":"Wild_Type","Treatment":"tamoxifen, 3day"},
"Additional sample data":{"Batch":"1a","Ion mode":"negative","RAW_FILE_NAME":"S3DWN4.mzML"}
},
{
"Subject ID":"WT22",
"Sample ID":"Serum3DWP1positive",
"Factors":{"Genotype":"Wild_Type","Treatment":"tamoxifen, 3day"},
"Additional sample data":{"Batch":"1a","Ion mode":"positive","RAW_FILE_NAME":"S3DWP1.mzML"}
},
{
"Subject ID":"WT23",
"Sample ID":"Serum3DWP2positive",
"Factors":{"Genotype":"Wild_Type","Treatment":"tamoxifen, 3day"},
"Additional sample data":{"Batch":"1a","Ion mode":"positive","RAW_FILE_NAME":"S3DWP2.mzML"}
},
{
"Subject ID":"WT24",
"Sample ID":"Serum3DWP3positive",
"Factors":{"Genotype":"Wild_Type","Treatment":"tamoxifen, 3day"},
"Additional sample data":{"Batch":"1a","Ion mode":"positive","RAW_FILE_NAME":"S3DWP3.mzML"}
},
{
"Subject ID":"WT25",
"Sample ID":"Serum3DWP4positive",
"Factors":{"Genotype":"Wild_Type","Treatment":"tamoxifen, 3day"},
"Additional sample data":{"Batch":"1a","Ion mode":"positive","RAW_FILE_NAME":"S3DWP4.mzML"}
},
{
"Subject ID":"WT3",
"Sample ID":"Kidney3MW1negative",
"Factors":{"Genotype":"Wild_Type","Treatment":"tamoxifen, 3month"},
"Additional sample data":{"Batch":"1a","Ion mode":"negative","RAW_FILE_NAME":"K3MW1.mzML"}
},
{
"Subject ID":"WT33",
"Sample ID":"Kidney3MW2negative",
"Factors":{"Genotype":"Wild_Type","Treatment":"tamoxifen, 3month"},
"Additional sample data":{"Batch":"1a","Ion mode":"negative","RAW_FILE_NAME":"K3MW2.mzML"}
},
{
"Subject ID":"WT34",
"Sample ID":"Kidney3MW3negative",
"Factors":{"Genotype":"Wild_Type","Treatment":"tamoxifen, 3month"},
"Additional sample data":{"Batch":"1a","Ion mode":"negative","RAW_FILE_NAME":"K3MW3.mzML"}
},
{
"Subject ID":"WT4",
"Sample ID":"Kidney3MW4negative",
"Factors":{"Genotype":"Wild_Type","Treatment":"tamoxifen, 3month"},
"Additional sample data":{"Batch":"1a","Ion mode":"negative","RAW_FILE_NAME":"K3MW4.mzML"}
},
{
"Subject ID":"WT3",
"Sample ID":"Serum3MWN1negative",
"Factors":{"Genotype":"Wild_Type","Treatment":"tamoxifen, 3month"},
"Additional sample data":{"Batch":"1a","Ion mode":"negative","RAW_FILE_NAME":"S3MWN1.mzML"}
},
{
"Subject ID":"WT31",
"Sample ID":"Serum3MWN2negative",
"Factors":{"Genotype":"Wild_Type","Treatment":"tamoxifen, 3month"},
"Additional sample data":{"Batch":"1a","Ion mode":"negative","RAW_FILE_NAME":"S3MWN2.mzML"}
},
{
"Subject ID":"WT32",
"Sample ID":"Serum3MWN3negative",
"Factors":{"Genotype":"Wild_Type","Treatment":"tamoxifen, 3month"},
"Additional sample data":{"Batch":"1a","Ion mode":"negative","RAW_FILE_NAME":"S3MWN3.mzML"}
},
{
"Subject ID":"WT4",
"Sample ID":"Serum3MWN4negative",
"Factors":{"Genotype":"Wild_Type","Treatment":"tamoxifen, 3month"},
"Additional sample data":{"Batch":"1a","Ion mode":"negative","RAW_FILE_NAME":"S3MWN4.mzML"}
},
{
"Subject ID":"WT3",
"Sample ID":"Serum3MWP1positive",
"Factors":{"Genotype":"Wild_Type","Treatment":"tamoxifen, 3month"},
"Additional sample data":{"Batch":"1a","Ion mode":"positive","RAW_FILE_NAME":"S3MWP1.mzML"}
},
{
"Subject ID":"WT31",
"Sample ID":"Serum3MWP2positive",
"Factors":{"Genotype":"Wild_Type","Treatment":"tamoxifen, 3month"},
"Additional sample data":{"Batch":"1a","Ion mode":"positive","RAW_FILE_NAME":"S3MWP2.mzML"}
},
{
"Subject ID":"WT32",
"Sample ID":"Serum3MWP3positive",
"Factors":{"Genotype":"Wild_Type","Treatment":"tamoxifen, 3month"},
"Additional sample data":{"Batch":"1a","Ion mode":"positive","RAW_FILE_NAME":"S3MWP3.mzML"}
},
{
"Subject ID":"WT4",
"Sample ID":"Serum3MWP4positive",
"Factors":{"Genotype":"Wild_Type","Treatment":"tamoxifen, 3month"},
"Additional sample data":{"Batch":"1a","Ion mode":"positive","RAW_FILE_NAME":"S3MWP4.mzML"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"serum and kidney were obtained from GCERRARaD females 3 days or 3 months post-tam (n=5/group) and age-matched wild-type females (n=4)","SAMPLE_TYPE":"Kidney; Serum"},

"TREATMENT":{"TREATMENT_SUMMARY":"Mutant and wild-type female mice were treated with tamoxifen for 3 days or 3 months."},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"To extract metabolites, frozen kidney cortices were weighed, and ca 20 mg of each cortex was added to a tube containing 650 μL of 80% methanol (diluted in dH2O). Sample tubes were placed in a bead homogenizer for 1 minute at a frequency of 30/s. Samples were then placed in a -20℃ freezer for 10 minutes, centrifuged for 10 minutes at 15,000 RPM in 4℃, and the supernatant was moved to a new tube. The remaining pellets were then re-extracted with 400 μL of 80% methanol, following the above procedure of homogenization and centrifugation. The supernatant was then added to the supernatant pool obtained from the first extraction. The pellet was re-extracted for a third time using 350 μL of 80% MeOH and supernatant was again added to the pool from the first two extractions. The supernatant pool was placed at -20℃ for 15 minutes, centrifuged for 20 minutes at 15,000 RPM, and transferred to a new tube. The methanolic extract samples were speed-vacuumed and reconstituted in 70% acetonitrile (diluted in dH2O) containing 0.025% acetic acid at a protein concentration of 3μg/μL. For serum preparation, samples were diluted 10-fold with 70% acetonitrile (diluted in dH2O) containing 0.025% acetic acid, and centrifuged for 20 minutes at 20,000 g."},

"CHROMATOGRAPHY":{"INSTRUMENT_NAME":"Agilent 1290 Infinity II","COLUMN_NAME":"MicroSolv Cogent Diamond Hydride (150 × 2.1 mm, 4.0 um)","COLUMN_TEMPERATURE":"25","FLOW_GRADIENT":"0-1 min, 99% B; 1-15 min, a linear gradient to 20% B; 15.1-29 min, 0% B; 29.1-37 min, 99% B","FLOW_RATE":"0.4mL/min","SOLVENT_A":"6 uM edta and 0.025% acetic acid in isopropanol:H2O (50:50)","SOLVENT_B":"6 uM edta and 5mM ammonium acetate in CH3CN: H2O (90:10)","CHROMATOGRAPHY_TYPE":"HILIC"},

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

"MS":{"INSTRUMENT_NAME":"Agilent 6550 QTOF","INSTRUMENT_TYPE":"QTOF","MS_TYPE":"ESI","MS_COMMENTS":"The serum samples have negative and positive mode data. The kidney samples have negative mode data. MassHunter B10 MassHunter B10 MassHunter Profinder (B10)","ION_MODE":"UNSPECIFIED"},

"MS_METABOLITE_DATA":{
"Units":"abundance",

"Data":[{"Metabolite":"Retinoic 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}