{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST000275","ANALYSIS_ID":"AN000438","VERSION":"1","CREATED_ON":"2016-09-17"},

"PROJECT":{"PROJECT_TITLE":"Metabolic analysis of Parp1 ko/wt Saline & Bleo Mouse Lung Fiboblasts and Human & Normal Lung Fiboblasts #2","PROJECT_TYPE":"Glycolysis/TCA/Nucleotide analysis (tissue/cells)","PROJECT_SUMMARY":"Hedgehog signaling plays important roles in cell development and In this study, the ability of Sonic Hedgehog (SHH) to induce myofibroblast was analyzed in isolated human lung fibroblasts, and its in vivo significance evaluated in rodent bleomycin-induced pulmonary fibrosis. The results showed SHH could induce myofibroblast differentiation in human lung fibroblasts in a and Gli1-dependent manner. Gel shift analysis, chromatin immunoprecipitation and site-directed mutagenesis revealed that a Gli1 binding consensus in the gene promoter was important for mediating SHH-induced myofibroblast Analysis of Hedgehog reemergence in vivo revealed that of all three Hedgehog only SHH was significantly induced in bleomycin-injured lung along with Gli1. induction of SHH was only noted in epithelial cells, and its expression was in lung fibroblasts or macrophages. Transforming growth factor (TGF)-? induced significantly in cultured alveolar epithelial cells, whereas SHH induced TGF-? lung fibroblasts. Pulmonary fibrosis and ?-smooth muscle actin (?-SMA) were significantly reduced in mice that were Smo deficient only in type I cells. Thus, the reemergence of SHH in epithelial cells could result in of myofibroblast differentiation in a Smo-dependent manner and subsequent Gli1 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"},

"STUDY":{"STUDY_TITLE":"Metabolic analysis of Parp1 ko/wt Saline & Bleo Mouse Lung Fiboblasts and Human & Normal Lung Fiboblasts (Part 2)","STUDY_TYPE":"Glycolysis/TCA/Nucleotide analysis. Ceramide analysis for parp1 wild type lung after saline or bleomycin treatment.","STUDY_SUMMARY":"This study is a part of series performed for the same researcher through grant program, so the publication is relevant reference for other studies ST000183)This specific experiment is a small pilot study to establish method it includes four biological replicas of identical cell cultures after the treatment and a single tissue sample.","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","NUM_GROUPS":"1","TOTAL_SUBJECTS":"5","STUDY_COMMENTS":"http://www.atsjournals.org/doi/full/10.1165/rcmb.2014-0108OC#.Vmb9VVWrRhE"},

"SUBJECT":{"SUBJECT_TYPE":"Animal","SUBJECT_SPECIES":"Mus musculus","TAXONOMY_ID":"10090","SPECIES_GROUP":"Mammal"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"-",
"Sample ID":"S00014994",
"Factors":{"Sample type":"Cell culture","Genetic background":"B6 wt","bleomycin":"yes"}
},
{
"Subject ID":"-",
"Sample ID":"S00014995",
"Factors":{"Sample type":"Cell culture","Genetic background":"B6 wt","bleomycin":"yes"}
},
{
"Subject ID":"-",
"Sample ID":"S00014996",
"Factors":{"Sample type":"Cell culture","Genetic background":"B6 wt","bleomycin":"yes"}
},
{
"Subject ID":"-",
"Sample ID":"S00014997",
"Factors":{"Sample type":"Cell culture","Genetic background":"B6 wt","bleomycin":"yes"}
},
{
"Subject ID":"-",
"Sample ID":"S00014998",
"Factors":{"Sample type":"Tissue","Genetic background":"B6 wt","bleomycin":"yes"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"-","SAMPLE_TYPE":"Cells"},

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

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

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_TYPE":"HILIC","INSTRUMENT_NAME":"Agilent 1260","COLUMN_NAME":"Phenomenex Luna NH2 (150 x 1mm, 3um)","METHODS_ID":"AQM020","METHODS_FILENAME":"QTOF-002-HILIC-35min-1mm.m"},

"ANALYSIS":{"ANALYSIS_TYPE":"MS","LABORATORY_NAME":"MRC2 (University of Michigan)","ACQUISITION_PARAMETERS_FILE":"Column1_solv1_jetstream+_grad9.m","PROCESSING_PARAMETERS_FILE":"EX00310-MassHunterQuant-GlyTCA-DataAnalysis-LCMS-Method.m"},

"MS":{"MS_COMMENTS":"-","INSTRUMENT_NAME":"Agilent 6530 QTOF","INSTRUMENT_TYPE":"QTOF","MS_TYPE":"ESI","ION_MODE":"NEGATIVE"},

"MS_METABOLITE_DATA":{
"Units":"µM (500µl of extraction solvent)",

"Data":[{"Metabolite":"2 or 3-phosphoglycerate_2PG/3PG","S00014994":"1.1577","S00014995":"1.1884","S00014996":"0.9990","S00014997":"0.7757","S00014998":"1.1878"},{"Metabolite":"6-Phosphogluconate","S00014994":"0.2863","S00014995":"0.2394","S00014996":"0.2879","S00014997":"0.1559","S00014998":"0.5618"},{"Metabolite":"Acetyl-CoA","S00014994":"0.1172","S00014995":"0.0648","S00014996":"0.0967","S00014997":"0.1000","S00014998":"0.0553"},{"Metabolite":"ADP","S00014994":"3.4110","S00014995":"3.5422","S00014996":"2.4469","S00014997":"2.0365","S00014998":"8.5675"},{"Metabolite":"AMP","S00014994":"5.5347","S00014995":"5.7634","S00014996":"3.5449","S00014997":"3.3430","S00014998":"303.2638"},{"Metabolite":"ATP","S00014994":"41.3260","S00014995":"36.0813","S00014996":"33.8644","S00014997":"30.5504","S00014998":"3.1217"},{"Metabolite":"Citrate or Isocitrate","S00014994":"32.8578","S00014995":"43.3185","S00014996":"35.1965","S00014997":"47.1062","S00014998":"24.9626"},{"Metabolite":"Erythrose 4-phosphate","S00014994":"2.8414","S00014995":"2.7062","S00014996":"2.4028","S00014997":"2.4877","S00014998":"16.5782"},{"Metabolite":"flavin adenine dinucleotide","S00014994":"0.0535","S00014995":"0.0524","S00014996":"0.0490","S00014997":"0.0475","S00014998":"0.4202"},{"Metabolite":"Fructose 1_6-bisphosphate","S00014994":"8.5102","S00014995":"7.9560","S00014996":"6.4152","S00014997":"5.8557","S00014998":"5.5311"},{"Metabolite":"Glucose 6-phosphate or fructose-6-phosphate","S00014994":"2.3811","S00014995":"1.7382","S00014996":"1.6978","S00014997":"1.4426","S00014998":"9.6583"},{"Metabolite":"Malate","S00014994":"11.3931","S00014995":"12.8468","S00014996":"10.8206","S00014997":"12.2637","S00014998":"20.9530"},{"Metabolite":"Nicotinamide Adenine Dinucleotide oxidized","S00014994":"1.8427","S00014995":"1.4685","S00014996":"1.5589","S00014997":"1.2770","S00014998":"0.0905"},{"Metabolite":"nicotinamide adenine dinucleotide phosphate oxidized","S00014994":"0.2135","S00014995":"0.1981","S00014996":"0.1568","S00014997":"0.1050","S00014998":"0.7036"},{"Metabolite":"nicotinamide adenine dinucleotide phosphate reduced","S00014994":"1.5520","S00014995":"1.2917","S00014996":"1.5221","S00014997":"1.7584","S00014998":"0.0968"},{"Metabolite":"Nicotinamide Adenine Dinucleotide reduced","S00014994":"0.2007","S00014995":"0.1058","S00014996":"0.2323","S00014997":"0.2723","S00014998":"0.3241"},{"Metabolite":"Phosphoenolpyruvate","S00014994":"0.6961","S00014995":"0.6103","S00014996":"0.7216","S00014997":"0.6450","S00014998":"0.2821"},{"Metabolite":"Ribose-5-phosphate or xylulose 5-phosphate","S00014994":"0.6749","S00014995":"0.6488","S00014996":"0.5681","S00014997":"0.5436","S00014998":"19.1959"},{"Metabolite":"sedoheptulose","S00014994":"","S00014995":"","S00014996":"","S00014997":"","S00014998":""},{"Metabolite":"Sedoheptulose 7-phosphate","S00014994":"1.0500","S00014995":"0.9529","S00014996":"0.8679","S00014997":"0.8941","S00014998":"6.9018"},{"Metabolite":"Sucrose","S00014994":"1.2615","S00014995":"1.5337","S00014996":"1.1406","S00014997":"1.5901","S00014998":"2.6906"}],

"Metabolites":[{"Metabolite":"2 or 3-phosphoglycerate_2PG/3PG","moverz_quant":"","ri":"","ri_type":"","pubchem_id":"724","inchi_key":"","kegg_id":"C00597","other_id":"2PG/3PG","other_id_type":"UM_Target_ID"},{"Metabolite":"6-Phosphogluconate","moverz_quant":"","ri":"","ri_type":"","pubchem_id":"91493","inchi_key":"","kegg_id":"C00345","other_id":"6PG","other_id_type":"UM_Target_ID"},{"Metabolite":"Acetyl-CoA","moverz_quant":"","ri":"","ri_type":"","pubchem_id":"444493","inchi_key":"","kegg_id":"C00024","other_id":"aCoA","other_id_type":"UM_Target_ID"},{"Metabolite":"ADP","moverz_quant":"","ri":"","ri_type":"","pubchem_id":"6022","inchi_key":"","kegg_id":"C00008","other_id":"ADP","other_id_type":"UM_Target_ID"},{"Metabolite":"AMP","moverz_quant":"","ri":"","ri_type":"","pubchem_id":"6083","inchi_key":"","kegg_id":"C00020","other_id":"AMP","other_id_type":"UM_Target_ID"},{"Metabolite":"ATP","moverz_quant":"","ri":"","ri_type":"","pubchem_id":"5957","inchi_key":"","kegg_id":"C00002","other_id":"ATP","other_id_type":"UM_Target_ID"},{"Metabolite":"Citrate or Isocitrate","moverz_quant":"","ri":"","ri_type":"","pubchem_id":"311","inchi_key":"","kegg_id":"C00158","other_id":"CIT/ICIT","other_id_type":"UM_Target_ID"},{"Metabolite":"Erythrose 4-phosphate","moverz_quant":"","ri":"","ri_type":"","pubchem_id":"122357","inchi_key":"","kegg_id":"C00279","other_id":"E4P","other_id_type":"UM_Target_ID"},{"Metabolite":"flavin adenine dinucleotide","moverz_quant":"","ri":"","ri_type":"","pubchem_id":"643975","inchi_key":"","kegg_id":"C00016","other_id":"FAD","other_id_type":"UM_Target_ID"},{"Metabolite":"Fructose 1,6-bisphosphate","moverz_quant":"","ri":"","ri_type":"","pubchem_id":"172313","inchi_key":"","kegg_id":"C00354","other_id":"FBP","other_id_type":"UM_Target_ID"},{"Metabolite":"Glucose 6-phosphate or fructose-6-phosphate","moverz_quant":"","ri":"","ri_type":"","pubchem_id":"5958","inchi_key":"","kegg_id":"C00092","other_id":"G6P/F6P","other_id_type":"UM_Target_ID"},{"Metabolite":"Malate","moverz_quant":"","ri":"","ri_type":"","pubchem_id":"222656","inchi_key":"","kegg_id":"C00149","other_id":"MAL","other_id_type":"UM_Target_ID"},{"Metabolite":"Nicotinamide Adenine Dinucleotide oxidized","moverz_quant":"","ri":"","ri_type":"","pubchem_id":"10897651","inchi_key":"","kegg_id":"C00003","other_id":"NAD","other_id_type":"UM_Target_ID"},{"Metabolite":"nicotinamide adenine dinucleotide phosphate oxidized","moverz_quant":"","ri":"","ri_type":"","pubchem_id":"5886","inchi_key":"","kegg_id":"C00006","other_id":"NADP","other_id_type":"UM_Target_ID"},{"Metabolite":"nicotinamide adenine dinucleotide phosphate reduced","moverz_quant":"","ri":"","ri_type":"","pubchem_id":"5886","inchi_key":"","kegg_id":"C00006","other_id":"NADPH","other_id_type":"UM_Target_ID"},{"Metabolite":"Nicotinamide Adenine Dinucleotide reduced","moverz_quant":"","ri":"","ri_type":"","pubchem_id":"439153","inchi_key":"","kegg_id":"C00004","other_id":"NADH","other_id_type":"UM_Target_ID"},{"Metabolite":"Phosphoenolpyruvate","moverz_quant":"","ri":"","ri_type":"","pubchem_id":"1005","inchi_key":"","kegg_id":"C00074","other_id":"PEP","other_id_type":"UM_Target_ID"},{"Metabolite":"Ribose-5-phosphate or xylulose 5-phosphate","moverz_quant":"","ri":"","ri_type":"","pubchem_id":"77982","inchi_key":"","kegg_id":"C00117","other_id":"R5P/X5P","other_id_type":"UM_Target_ID"},{"Metabolite":"sedoheptulose","moverz_quant":"","ri":"","ri_type":"","pubchem_id":"102926","inchi_key":"","kegg_id":"","other_id":"SED","other_id_type":"UM_Target_ID"},{"Metabolite":"Sedoheptulose 7-phosphate","moverz_quant":"","ri":"","ri_type":"","pubchem_id":"165007","inchi_key":"","kegg_id":"C05382","other_id":"S7P","other_id_type":"UM_Target_ID"},{"Metabolite":"Sucrose","moverz_quant":"","ri":"","ri_type":"","pubchem_id":"5988","inchi_key":"","kegg_id":"C00089","other_id":"SUC","other_id_type":"UM_Target_ID"}]
}

}