{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST000143","ANALYSIS_ID":"AN000227","VERSION":"1","CREATED_ON":"01-15-2019"},

"PROJECT":{"PROJECT_TITLE":"Metabolic analysis of Parp1 ko/wt Saline & Bleo Mouse Lung Fibroblasts and Human IPF & Normal Lung Fibroblasts","PROJECT_TYPE":"Glycolysis/TCA/Nucleotide analysis (tissue/cells)","PROJECT_SUMMARY":"Hedgehog signaling plays important roles in cell development and differentiation. In this study, the ability of Sonic Hedgehog (SHH) to induce myofibroblast differentiation was analyzed in isolated human lung fibroblasts, and its in vivo significance was evaluated in rodent bleomycin-induced pulmonary fibrosis. The results showed that SHH could induce myofibroblast differentiation in human lung fibroblasts in a Smo- and Gli1-dependent manner. Gel shift analysis, chromatin immunoprecipitation assay, and site-directed mutagenesis revealed that a Gli1 binding consensus in the ?-SMA gene promoter was important for mediating SHH-induced myofibroblast differentiation. Analysis of Hedgehog reemergence in vivo revealed that of all three Hedgehog isoforms, only SHH was significantly induced in bleomycin-injured lung along with Gli1. The induction of SHH was only noted in epithelial cells, and its expression was undetectable in lung fibroblasts or macrophages. Transforming growth factor (TGF)-? induced SHH significantly in cultured alveolar epithelial cells, whereas SHH induced TGF-? in lung fibroblasts. Pulmonary fibrosis and ?-smooth muscle actin (?-SMA) expression were significantly reduced in mice that were Smo deficient only in type I collagen–expressing cells. Thus, the reemergence of SHH in epithelial cells could result in induction of myofibroblast differentiation in a Smo-dependent manner and subsequent Gli1 activation of the ?-SMA promoter.","INSTITUTE":"University of Michigan","DEPARTMENT":"Deaprtment of Pathology","LABORATORY":"Sem H. Phan","LAST_NAME":"Hu","FIRST_NAME":"Biao","ADDRESS":"Ann Arbor, MI","EMAIL":"biaohu@med.umich.edu","PHONE":"734-7635731","DOI":"http://dx.doi.org/10.21228/M8359Z"},

"STUDY":{"STUDY_TITLE":"Metabolic analysis of Normal Mouse Lung Fiboblasts with/without TGFbeta treatment (Part 1)","STUDY_TYPE":"Glycolysis/TCA/Nucleotide analysis (tissue/cells)","STUDY_SUMMARY":"This study is a part of series performed for the same researcher through pilot/feasibility grant program, so the publication is relevant reference for other studies, see the project for this study. This specific experiment is a small pilot study to establish method performance, it includes four biological replicas of identical cell cultures after the identical treatment and a single tissue sample.","INSTITUTE":"University of Michigan","DEPARTMENT":"Biomedical Research Core Facilities","LABORATORY":"Metabolomics core","LAST_NAME":"Kachman","FIRST_NAME":"Maureen","ADDRESS":"6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714","EMAIL":"mkachman@umich.edu","PHONE":"-"},

"SUBJECT":{"SUBJECT_TYPE":"Animal","SUBJECT_SPECIES":"Mus musculus","TAXONOMY_ID":"10090","SPECIES_GROUP":"Mammal"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"SU0003983",
"Sample ID":"S00014557",
"Factors":{"Genotype":"parp1 ko","Treatment":"bleomycin"}
},
{
"Subject ID":"SU0003984",
"Sample ID":"S00014558",
"Factors":{"Genotype":"parp1 ko","Treatment":"bleomycin"}
},
{
"Subject ID":"SU0003985",
"Sample ID":"S00014559",
"Factors":{"Genotype":"parp1 ko","Treatment":"bleomycin"}
},
{
"Subject ID":"SU0003994",
"Sample ID":"S00014568",
"Factors":{"Genotype":"parp1 ko","Treatment":"bleomycin"}
},
{
"Subject ID":"SU0003995",
"Sample ID":"S00014569",
"Factors":{"Genotype":"parp1 ko","Treatment":"bleomycin"}
},
{
"Subject ID":"SU0004004",
"Sample ID":"S00014578",
"Factors":{"Genotype":"parp1 ko","Treatment":"bleomycin"}
},
{
"Subject ID":"SU0004005",
"Sample ID":"S00014579",
"Factors":{"Genotype":"parp1 ko","Treatment":"bleomycin"}
},
{
"Subject ID":"SU0004006",
"Sample ID":"S00014580",
"Factors":{"Genotype":"parp1 ko","Treatment":"bleomycin"}
},
{
"Subject ID":"SU0003980",
"Sample ID":"S00014554",
"Factors":{"Genotype":"parp1 ko","Treatment":"saline"}
},
{
"Subject ID":"SU0003981",
"Sample ID":"S00014555",
"Factors":{"Genotype":"parp1 ko","Treatment":"saline"}
},
{
"Subject ID":"SU0003982",
"Sample ID":"S00014556",
"Factors":{"Genotype":"parp1 ko","Treatment":"saline"}
},
{
"Subject ID":"SU0003992",
"Sample ID":"S00014566",
"Factors":{"Genotype":"parp1 ko","Treatment":"saline"}
},
{
"Subject ID":"SU0003993",
"Sample ID":"S00014567",
"Factors":{"Genotype":"parp1 ko","Treatment":"saline"}
},
{
"Subject ID":"SU0004001",
"Sample ID":"S00014575",
"Factors":{"Genotype":"parp1 ko","Treatment":"saline"}
},
{
"Subject ID":"SU0004002",
"Sample ID":"S00014576",
"Factors":{"Genotype":"parp1 ko","Treatment":"saline"}
},
{
"Subject ID":"SU0004003",
"Sample ID":"S00014577",
"Factors":{"Genotype":"parp1 ko","Treatment":"saline"}
},
{
"Subject ID":"SU0003989",
"Sample ID":"S00014563",
"Factors":{"Genotype":"parp1 wt","Treatment":"bleomycin"}
},
{
"Subject ID":"SU0003990",
"Sample ID":"S00014564",
"Factors":{"Genotype":"parp1 wt","Treatment":"bleomycin"}
},
{
"Subject ID":"SU0003991",
"Sample ID":"S00014565",
"Factors":{"Genotype":"parp1 wt","Treatment":"bleomycin"}
},
{
"Subject ID":"SU0003998",
"Sample ID":"S00014572",
"Factors":{"Genotype":"parp1 wt","Treatment":"bleomycin"}
},
{
"Subject ID":"SU0003999",
"Sample ID":"S00014573",
"Factors":{"Genotype":"parp1 wt","Treatment":"bleomycin"}
},
{
"Subject ID":"SU0004000",
"Sample ID":"S00014574",
"Factors":{"Genotype":"parp1 wt","Treatment":"bleomycin"}
},
{
"Subject ID":"SU0003986",
"Sample ID":"S00014560",
"Factors":{"Genotype":"parp1 wt","Treatment":"saline"}
},
{
"Subject ID":"SU0003987",
"Sample ID":"S00014561",
"Factors":{"Genotype":"parp1 wt","Treatment":"saline"}
},
{
"Subject ID":"SU0003988",
"Sample ID":"S00014562",
"Factors":{"Genotype":"parp1 wt","Treatment":"saline"}
},
{
"Subject ID":"SU0003996",
"Sample ID":"S00014570",
"Factors":{"Genotype":"parp1 wt","Treatment":"saline"}
},
{
"Subject ID":"SU0003997",
"Sample ID":"S00014571",
"Factors":{"Genotype":"parp1 wt","Treatment":"saline"}
},
{
"Subject ID":"SU0004007",
"Sample ID":"S00014581",
"Factors":{"Genotype":"parp1 wt","Treatment":"saline"}
},
{
"Subject ID":"SU0004008",
"Sample ID":"S00014582",
"Factors":{"Genotype":"parp1 wt","Treatment":"saline"}
},
{
"Subject ID":"SU0004009",
"Sample ID":"S00014583",
"Factors":{"Genotype":"parp1 wt","Treatment":"saline"}
}
],
"COLLECTION":{"SAMPLE_TYPE":"Tissues","COLLECTION_SUMMARY":"-"},

"TREATMENT":{"TREATMENT_SUMMARY":"-"},

"SAMPLEPREP":{"SAMPLEPREP_PROTOCOL_FILENAME":"Gly-TCA-nucleotides_analysis_protocol-2015-03-09.docx","SAMPLEPREP_SUMMARY":"-"},

"CHROMATOGRAPHY":{"METHODS_ID":"AQM011","METHODS_FILENAME":"ALPHA_KETO_ACIDS-FULL.M.zip","INSTRUMENT_NAME":"Agilent 7890A","COLUMN_NAME":"Agilent DB5-MS (30m × 0.25mm, 0.25um)","CHROMATOGRAPHY_TYPE":"GC"},

"ANALYSIS":{"LABORATORY_NAME":"MRC2 (University of Michigan)","ANALYSIS_TYPE":"MS","ACQUISITION_PARAMETERS_FILE":"ALPHA_KETO_ACIDS-FULL.M.zip","PROCESSING_PARAMETERS_FILE":"EX00294-MassHunterQuant-GlyTCA-GCMS-DataAnalysis-Method.m.zip"},

"MS":{"MS_COMMENTS":"-","INSTRUMENT_NAME":"Agilent 5975C","INSTRUMENT_TYPE":"Single quadrupole","MS_TYPE":"EI","ION_MODE":"POSITIVE","TUBE_LENS_VOLTAGE":"Positive"},

"MS_METABOLITE_DATA":{
"Units":"uM",

"Data":[{"Metabolite":"Alanine","S00014557":"151.6573","S00014558":"70.4766","S00014559":"93.5807","S00014568":"111.4252","S00014569":"139.9279","S00014578":"167.2569","S00014579":"205.0150","S00014580":"90.1871","S00014554":"7.7040","S00014555":"82.4592","S00014556":"30.6312","S00014566":"25.5918","S00014567":"76.4968","S00014575":"95.2423","S00014576":"155.7659","S00014577":"128.3495","S00014563":"90.5514","S00014564":"63.8067","S00014565":"72.5396","S00014572":"181.4594","S00014573":"108.1661","S00014574":"105.7941","S00014560":"55.5827","S00014561":"35.3740","S00014562":"80.7843","S00014570":"134.3805","S00014571":"113.6705","S00014581":"123.8192","S00014582":"75.1341","S00014583":"44.2565"},{"Metabolite":"alpha-Ketoglutarate","S00014557":"7.1708","S00014558":"7.0555","S00014559":"4.8385","S00014568":"8.8545","S00014569":"6.4383","S00014578":"7.5234","S00014579":"8.4837","S00014580":"6.2941","S00014554":"1.2637","S00014555":"10.8507","S00014556":"6.3356","S00014566":"7.6072","S00014567":"11.2267","S00014575":"10.7315","S00014576":"15.2899","S00014577":"15.2920","S00014563":"6.4578","S00014564":"7.2312","S00014565":"6.8530","S00014572":"7.5326","S00014573":"6.4014","S00014574":"6.5092","S00014560":"8.6642","S00014561":"7.3092","S00014562":"11.8568","S00014570":"16.6321","S00014571":"13.3534","S00014581":"12.8941","S00014582":"14.1187","S00014583":"9.2709"},{"Metabolite":"Aspartate","S00014557":"2076.4871","S00014558":"797.7439","S00014559":"1433.4756","S00014568":"1242.7894","S00014569":"1616.6492","S00014578":"349.7478","S00014579":"2231.0293","S00014580":"1320.6448","S00014554":"188.9277","S00014555":"1959.6168","S00014556":"650.3874","S00014566":"683.4647","S00014567":"1950.4351","S00014575":"1642.2770","S00014576":"3256.4948","S00014577":"3183.1172","S00014563":"1255.9257","S00014564":"730.8475","S00014565":"1014.8004","S00014572":"802.7163","S00014573":"884.0014","S00014574":"853.8910","S00014560":"1169.0253","S00014561":"846.5137","S00014562":"2134.1592","S00014570":"2205.6471","S00014571":"2677.9243","S00014581":"2065.5850","S00014582":"2104.9137","S00014583":"1540.6600"},{"Metabolite":"Fumarate","S00014557":"17.0088","S00014558":"11.6572","S00014559":"9.0879","S00014568":"12.3454","S00014569":"15.2743","S00014578":"19.2316","S00014579":"17.1799","S00014580":"9.3336","S00014554":"0.9722","S00014555":"11.5210","S00014556":"4.9353","S00014566":"4.8900","S00014567":"15.1165","S00014575":"17.4668","S00014576":"32.6831","S00014577":"23.4230","S00014563":"9.8914","S00014564":"14.7183","S00014565":"10.4935","S00014572":"25.6170","S00014573":"17.2919","S00014574":"13.5918","S00014560":"7.2624","S00014561":"5.0299","S00014562":"13.8872","S00014570":"23.7657","S00014571":"21.7977","S00014581":"15.3666","S00014582":"21.3472","S00014583":"10.0972"},{"Metabolite":"Glutamate","S00014557":"2105.7375","S00014558":"1099.1217","S00014559":"1469.9426","S00014568":"1842.7389","S00014569":"3276.6622","S00014578":"627.2081","S00014579":"2256.9272","S00014580":"1173.1735","S00014554":"160.3561","S00014555":"1701.1911","S00014556":"576.3003","S00014566":"1143.0470","S00014567":"1493.4309","S00014575":"1303.6415","S00014576":"2794.0158","S00014577":"2330.5132","S00014563":"1427.3856","S00014564":"1568.6731","S00014565":"1539.0837","S00014572":"1239.6388","S00014573":"1353.0150","S00014574":"1105.3898","S00014560":"956.7064","S00014561":"737.4067","S00014562":"1818.2787","S00014570":"1923.7723","S00014571":"2136.3574","S00014581":"1550.7936","S00014582":"1499.0787","S00014583":"1386.2061"},{"Metabolite":"Glutamine","S00014557":"","S00014558":"","S00014559":"","S00014568":"","S00014569":"","S00014578":"","S00014579":"","S00014580":"","S00014554":"","S00014555":"","S00014556":"","S00014566":"","S00014567":"","S00014575":"","S00014576":"","S00014577":"","S00014563":"","S00014564":"","S00014565":"","S00014572":"","S00014573":"","S00014574":"","S00014560":"","S00014561":"","S00014562":"","S00014570":"","S00014571":"","S00014581":"","S00014582":"","S00014583":""},{"Metabolite":"Lactate","S00014557":"251.1005","S00014558":"158.1682","S00014559":"130.6085","S00014568":"166.7536","S00014569":"222.1973","S00014578":"892.3098","S00014579":"261.5111","S00014580":"101.4923","S00014554":"8.1847","S00014555":"116.0776","S00014556":"48.8403","S00014566":"36.7356","S00014567":"117.2674","S00014575":"121.9344","S00014576":"219.1280","S00014577":"146.0706","S00014563":"121.9681","S00014564":"152.3817","S00014565":"134.0089","S00014572":"1458.5798","S00014573":"257.9958","S00014574":"222.2661","S00014560":"87.8774","S00014561":"32.1373","S00014562":"88.4476","S00014570":"161.6987","S00014571":"152.1650","S00014581":"114.2767","S00014582":"116.7061","S00014583":"36.3362"},{"Metabolite":"Oxaloacetate","S00014557":"","S00014558":"","S00014559":"","S00014568":"","S00014569":"","S00014578":"","S00014579":"","S00014580":"","S00014554":"","S00014555":"","S00014556":"","S00014566":"","S00014567":"","S00014575":"","S00014576":"","S00014577":"","S00014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}

}