{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST000274","ANALYSIS_ID":"AN000437","VERSION":"1","CREATED_ON":"2016-09-17"},

"PROJECT":{"PROJECT_TITLE":"HIF 1 alpha","PROJECT_SUMMARY":"Glycolysis/TCA/Nucleotide analysis (AEC cells)","INSTITUTE":"University of Michigan","DEPARTMENT":"Surgery","LABORATORY":"Raghavendran Lab","LAST_NAME":"Raghavendran","FIRST_NAME":"Krishnan","ADDRESS":"Ann Arbor, MI","EMAIL":"kraghave@umich.edu","PHONE":"734-615-7142"},

"STUDY":{"STUDY_TITLE":"HIF 1 alpha type 2 cells metabolomics","STUDY_TYPE":"Glycolysis/TCA/Nucleotide analysis (tissue/cells)","STUDY_SUMMARY":"Lung contusion is a major risk factor for the development of acute respiratory syndrome. Hypoxia-inducible factor-1? is the primary transcription factor that responsible for regulating the cellular response to changes in oxygen tension. set to determine if hypoxia-inducible factor-1? plays a role in the of acute inflammatory response and injury in lung contusion.Nonlethal unilateral lung contusion was induced in a hypoxia reporter mouse model and 2 cell-specific hypoxia-inducible factor-1? conditional knockout mice. The mice killed at 5-, 24-, 48-, and 72-hour time points, and the extent of systemic and hypoxia was assessed. In addition, injury and inflammation were assessed by bronchoalveolar lavage cells (flow cytometry and cytospin), albumin injury), and cytokines (inflammation). Isolated type 2 cells from the factor-1? conditional knockout mice were isolated and evaluated for cytokines following lung contusion. Finally, the role of nuclear factor-?B and as intermediates in this interaction was studied.","INSTITUTE":"University of Michigan","DEPARTMENT":"Surgery","LABORATORY":"Raghavendran Lab","LAST_NAME":"Thomas","FIRST_NAME":"Bivin","ADDRESS":"Ann Arbor, MI","EMAIL":"bthomas@umich.edu","PHONE":"734-615-7142","NUM_GROUPS":"4","TOTAL_SUBJECTS":"8","STUDY_COMMENTS":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4245055/ : HIF1 (+/+) stands for reporter mouse modelHIF1 (-/-) stands for type 2 cell-specific factor-1? conditional knockout"},

"SUBJECT":{"SUBJECT_TYPE":"Animal","SUBJECT_SPECIES":"Mus musculus","TAXONOMY_ID":"10090","SPECIES_GROUP":"Mammal"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"-",
"Sample ID":"S00014948",
"Factors":{"Genotype":"HIF1 (-/-)","Treatment":"Control"}
},
{
"Subject ID":"-",
"Sample ID":"S00014949",
"Factors":{"Genotype":"HIF1 (-/-)","Treatment":"Control"}
},
{
"Subject ID":"-",
"Sample ID":"S00014944",
"Factors":{"Genotype":"HIF1 (+/+)","Treatment":"Control"}
},
{
"Subject ID":"-",
"Sample ID":"S00014945",
"Factors":{"Genotype":"HIF1 (+/+)","Treatment":"Control"}
},
{
"Subject ID":"-",
"Sample ID":"S00014950",
"Factors":{"Genotype":"HIF1 (-/-)","Treatment":"Lung contusion, 24h"}
},
{
"Subject ID":"-",
"Sample ID":"S00014951",
"Factors":{"Genotype":"HIF1 (-/-)","Treatment":"Lung contusion, 24h"}
},
{
"Subject ID":"-",
"Sample ID":"S00014946",
"Factors":{"Genotype":"HIF1 (+/+)","Treatment":"Lung contusion, 24h"}
},
{
"Subject ID":"-",
"Sample ID":"S00014947",
"Factors":{"Genotype":"HIF1 (+/+)","Treatment":"Lung contusion, 24h"}
},
{
"Subject ID":"-",
"Sample ID":"S00020491",
"Factors":{"Genotype":"Pooled sample","Treatment":"Pooled cells"}
}
],
"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-No_Insert.m"},

"ANALYSIS":{"ANALYSIS_TYPE":"MS","LABORATORY_NAME":"MRC2 (University of Michigan)","ACQUISITION_PARAMETERS_FILE":"QTOF-002-HILIC-35min-1mm-No_Insert.m","PROCESSING_PARAMETERS_FILE":"EX00307-MassHunterQuant-GlyTCA-LCMS-DataAnalysis-Method.m"},

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

"MS_METABOLITE_DATA":{
"Units":"pmol/µg protein",

"Data":[{"Metabolite":"2 or 3-phosphoglycerate_2PG/3PG","S00014948":"0.4923","S00014949":"0.7110","S00014944":"0.8611","S00014945":"2.2346","S00014950":"1.0397","S00014951":"0.6412","S00014946":"2.3720","S00014947":"1.7139"},{"Metabolite":"6-Phosphogluconate","S00014948":"0.2709","S00014949":"","S00014944":"0.3188","S00014945":"0.3173","S00014950":"0.1616","S00014951":"0.0869","S00014946":"0.1352","S00014947":"0.2018"},{"Metabolite":"Acetyl-CoA","S00014948":"0.2649","S00014949":"0.2697","S00014944":"0.4070","S00014945":"0.7993","S00014950":"0.5029","S00014951":"0.2225","S00014946":"0.8440","S00014947":"0.5996"},{"Metabolite":"adenosine","S00014948":"1.8831","S00014949":"1.2545","S00014944":"10.3089","S00014945":"17.6305","S00014950":"38.8862","S00014951":"19.4795","S00014946":"7.2443","S00014947":"28.7146"},{"Metabolite":"ADP","S00014948":"11.5581","S00014949":"19.0367","S00014944":"10.9149","S00014945":"21.4723","S00014950":"4.7700","S00014951":"1.8193","S00014946":"37.5566","S00014947":"20.6323"},{"Metabolite":"AMP","S00014948":"398.5276","S00014949":"488.6746","S00014944":"1150.7201","S00014945":"1805.8813","S00014950":"1360.7255","S00014951":"892.2914","S00014946":"1090.6977","S00014947":"1167.0805"},{"Metabolite":"ATP","S00014948":"6.4894","S00014949":"10.4910","S00014944":"3.7231","S00014945":"7.8167","S00014950":"2.0310","S00014951":"0.8154","S00014946":"54.0677","S00014947":"16.8000"},{"Metabolite":"Citrate or Isocitrate","S00014948":"24.5583","S00014949":"34.5114","S00014944":"49.4800","S00014945":"78.4312","S00014950":"62.8255","S00014951":"44.1718","S00014946":"112.6494","S00014947":"93.5648"},{"Metabolite":"flavin adenine dinucleotide","S00014948":"0.2822","S00014949":"0.3058","S00014944":"0.4543","S00014945":"0.7097","S00014950":"0.6850","S00014951":"0.3389","S00014946":"0.8508","S00014947":"0.6878"},{"Metabolite":"Fructose 1_6-bisphosphate","S00014948":"9.8186","S00014949":"14.4112","S00014944":"13.1371","S00014945":"13.1023","S00014950":"11.0040","S00014951":"6.7597","S00014946":"33.2205","S00014947":"19.3991"},{"Metabolite":"Glucose 6-phosphate or fructose-6-phosphate","S00014948":"9.2556","S00014949":"10.2307","S00014944":"21.5468","S00014945":"27.8144","S00014950":"15.8916","S00014951":"11.5451","S00014946":"28.2213","S00014947":"24.5232"},{"Metabolite":"Lactate","S00014948":"26.6605","S00014949":"22.6068","S00014944":"26.6727","S00014945":"26.7212","S00014950":"35.9952","S00014951":"33.4328","S00014946":"47.9150","S00014947":"26.5791"},{"Metabolite":"Malate","S00014948":"88.9937","S00014949":"88.4946","S00014944":"109.7923","S00014945":"175.8938","S00014950":"132.4842","S00014951":"96.7829","S00014946":"215.3524","S00014947":"176.9606"},{"Metabolite":"Nicotinamide Adenine Dinucleotide oxidized","S00014948":"3.4073","S00014949":"4.3689","S00014944":"5.1978","S00014945":"9.8458","S00014950":"5.4708","S00014951":"2.6117","S00014946":"12.1045","S00014947":"8.8395"},{"Metabolite":"nicotinamide adenine dinucleotide phosphate oxidized","S00014948":"1.9389","S00014949":"2.6738","S00014944":"3.6820","S00014945":"6.0889","S00014950":"2.6102","S00014951":"1.2883","S00014946":"4.8533","S00014947":"3.8668"},{"Metabolite":"nicotinamide adenine dinucleotide phosphate reduced","S00014948":"","S00014949":"","S00014944":"2.0027","S00014945":"4.0838","S00014950":"","S00014951":"","S00014946":"23.8938","S00014947":"15.8830"},{"Metabolite":"Nicotinamide Adenine Dinucleotide reduced","S00014948":"","S00014949":"","S00014944":"0.1178","S00014945":"","S00014950":"","S00014951":"","S00014946":"","S00014947":"0.2256"},{"Metabolite":"Phosphoenolpyruvate","S00014948":"","S00014949":"","S00014944":"","S00014945":"","S00014950":"","S00014951":"","S00014946":"","S00014947":"0.3793"},{"Metabolite":"Sucrose","S00014948":"210.2357","S00014949":"40.3946","S00014944":"62.2260","S00014945":"58.8831","S00014950":"82.2040","S00014951":"54.6808","S00014946":"101.3678","S00014947":"119.8509"}],

"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":"adenosine","moverz_quant":"","ri":"","ri_type":"","pubchem_id":"60961","inchi_key":"","kegg_id":"C00212","other_id":"Adenosine","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":"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":"Lactate","moverz_quant":"","ri":"","ri_type":"","pubchem_id":"107689","inchi_key":"","kegg_id":"C00186","other_id":"LAC","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":"Sucrose","moverz_quant":"","ri":"","ri_type":"","pubchem_id":"5988","inchi_key":"","kegg_id":"C00089","other_id":"SUC","other_id_type":"UM_Target_ID"}]
}

}