{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST000313","ANALYSIS_ID":"AN000499","VERSION":"1","CREATED_ON":"January 13, 2016, 4:44 pm"},

"PROJECT":{"PROJECT_TITLE":"Muscle Clock knock out metabolic changes","PROJECT_SUMMARY":"Inducible KO of Bmal1 in skeletal muscle; we see transcriptional changes suggesting significant effects in TCA/substrate metabolism","INSTITUTE":"University of Kentucky","DEPARTMENT":"Physiology","LABORATORY":"Esser Lab","LAST_NAME":"Esser","FIRST_NAME":"Karyn","ADDRESS":"Lexington, KY","EMAIL":"karyn.esser@uky.edu","PHONE":"859-323-8107"},

"STUDY":{"STUDY_TITLE":"Muscle Clock knock out mice metabolic changes (iMSBmal1-Exp1)","STUDY_TYPE":"Regular","STUDY_SUMMARY":"My lab studies the function of the molecular clocks in skeletal muscle. We have an inducible genetic mouse model (C57Bl6 background) in which we knock out the core clock gene, Bmal1, only in adult skeletal muscle after treatment with tamoxifen. We have found that the mice maintain body mass but lose fat mass at 10 weeks after loss of Bmal1. We have done expression profiling on the skeletal muscles and gene expression changes (insulin signaling, CHO metabolism, fat metabolism) suggest significant changes in substrate metabolism. To analyze TCA, CHO metabolites we have collected gastrocnemius muscles from these mice following instructions from Dr. Burant. Mice were anaesthetized with isoflurane, the gastrocnemius muscle dissected and flash frozen with tongs cooled with liquid N2. They have been stored in cryovials in our -80 freezer for 2 months.","INSTITUTE":"University of Michigan","DEPARTMENT":"Biomedical Research Facilities","LABORATORY":"Metabolomics core","LAST_NAME":"Kachman","FIRST_NAME":"Maureen","ADDRESS":"6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714","EMAIL":"mkachman@med.umich.edu","PHONE":"(734) 232-8175","NUM_GROUPS":"2","TOTAL_SUBJECTS":"14"},

"SUBJECT":{"SUBJECT_TYPE":"Animal","SUBJECT_SPECIES":"Mus musculus","TAXONOMY_ID":"10090"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"SU0012034",
"Sample ID":"S00017942",
"Factors":{"muscle Bmal1":"Bmal1 positive"}
},
{
"Subject ID":"SU0012035",
"Sample ID":"S00017943",
"Factors":{"muscle Bmal1":"Bmal1 positive"}
},
{
"Subject ID":"SU0012036",
"Sample ID":"S00017944",
"Factors":{"muscle Bmal1":"Bmal1 positive"}
},
{
"Subject ID":"SU0012037",
"Sample ID":"S00017945",
"Factors":{"muscle Bmal1":"Bmal1 positive"}
},
{
"Subject ID":"SU0012038",
"Sample ID":"S00017946",
"Factors":{"muscle Bmal1":"Bmal1 positive"}
},
{
"Subject ID":"SU0012039",
"Sample ID":"S00017947",
"Factors":{"muscle Bmal1":"Bmal1 positive"}
},
{
"Subject ID":"SU0012040",
"Sample ID":"S00017948",
"Factors":{"muscle Bmal1":"Bmal1 positive"}
},
{
"Subject ID":"SU0012041",
"Sample ID":"S00017949",
"Factors":{"muscle Bmal1":"Bmal1 negative"}
},
{
"Subject ID":"SU0012042",
"Sample ID":"S00017950",
"Factors":{"muscle Bmal1":"Bmal1 negative"}
},
{
"Subject ID":"SU0012043",
"Sample ID":"S00017951",
"Factors":{"muscle Bmal1":"Bmal1 negative"}
},
{
"Subject ID":"SU0012044",
"Sample ID":"S00017952",
"Factors":{"muscle Bmal1":"Bmal1 negative"}
},
{
"Subject ID":"SU0012045",
"Sample ID":"S00017953",
"Factors":{"muscle Bmal1":"Bmal1 negative"}
},
{
"Subject ID":"SU0012046",
"Sample ID":"S00017954",
"Factors":{"muscle Bmal1":"Bmal1 negative"}
},
{
"Subject ID":"SU0012047",
"Sample ID":"S00017955",
"Factors":{"muscle Bmal1":"Bmal1 negative"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"None","SAMPLE_TYPE":"Muscle, Skeletal"},

"TREATMENT":{"TREATMENT_SUMMARY":"None"},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"None","SAMPLEPREP_PROTOCOL_FILENAME":"Glycolysis-TCA-nucleotides-20150324.docx"},

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

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

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

"MS_METABOLITE_DATA":{
"Units":"µM",

"Data":[{"Metabolite":"2 or 3-phosphoglycerate","S00017942":"2.478","S00017943":"3.434","S00017944":"3.054","S00017945":"2.490","S00017946":"0.427","S00017947":"4.708","S00017948":"2.153","S00017949":"0.992","S00017950":"0.435","S00017951":"1.144","S00017952":"0.449","S00017953":"0.725","S00017954":"3.069","S00017955":"1.650"},{"Metabolite":"6-phosphogluconate","S00017942":"0.061","S00017943":"0.058","S00017944":"0.066","S00017945":"0.064","S00017946":"0.047","S00017947":"0.021","S00017948":"0.021","S00017949":"0.034","S00017950":"0.042","S00017951":"0.047","S00017952":"0.034","S00017953":"0.035","S00017954":"0.097","S00017955":"0.055"},{"Metabolite":"acetyl-coa","S00017942":"0.007","S00017943":"0.005","S00017944":"0.003","S00017945":"0.001","S00017946":"0.007","S00017947":"0.001","S00017948":"0.001","S00017949":"0.007","S00017950":"0.005","S00017951":"0.003","S00017952":"0.002","S00017953":"0.002","S00017954":"0.009","S00017955":"0.005"},{"Metabolite":"adenosine diphosphate","S00017942":"3.319","S00017943":"3.311","S00017944":"1.703","S00017945":"3.763","S00017946":"2.918","S00017947":"2.187","S00017948":"2.623","S00017949":"2.792","S00017950":"2.744","S00017951":"2.384","S00017952":"3.105","S00017953":"2.850","S00017954":"1.857","S00017955":"2.605"},{"Metabolite":"Alpha-ketoglutaric acid","S00017942":"1.401","S00017943":"1.643","S00017944":"1.267","S00017945":"","S00017946":"1.185","S00017947":"1.130","S00017948":"1.499","S00017949":"1.144","S00017950":"1.280","S00017951":"1.314","S00017952":"1.118","S00017953":"1.196","S00017954":"0.907","S00017955":"1.263"},{"Metabolite":"adenosine monophosphate","S00017942":"0.962","S00017943":"0.285","S00017944":"0.110","S00017945":"1.290","S00017946":"1.339","S00017947":"0.131","S00017948":"0.161","S00017949":"1.242","S00017950":"0.472","S00017951":"0.713","S00017952":"0.343","S00017953":"1.525","S00017954":"0.224","S00017955":"0.361"},{"Metabolite":"adenosine triphosphate","S00017942":"25.769","S00017943":"30.191","S00017944":"0.336","S00017945":"3.276","S00017946":"0.470","S00017947":"0.287","S00017948":"0.312","S00017949":"0.523","S00017950":"0.401","S00017951":"0.773","S00017952":"0.589","S00017953":"0.486","S00017954":"0.372","S00017955":"0.700"},{"Metabolite":"citrate or isocitrate","S00017942":"14.002","S00017943":"14.052","S00017944":"14.253","S00017945":"14.059","S00017946":"14.102","S00017947":"14.285","S00017948":"13.781","S00017949":"14.223","S00017950":"14.198","S00017951":"14.193","S00017952":"14.155","S00017953":"14.199","S00017954":"14.055","S00017955":"14.107"},{"Metabolite":"erythrose 4-phosphate","S00017942":"11.323","S00017943":"16.833","S00017944":"3.172","S00017945":"7.087","S00017946":"1.624","S00017947":"5.362","S00017948":"2.727","S00017949":"3.496","S00017950":"6.013","S00017951":"3.859","S00017952":"4.240","S00017953":"16.382","S00017954":"42.583","S00017955":"14.758"},{"Metabolite":"flavin adenine dinucleotide","S00017942":"0.152","S00017943":"0.164","S00017944":"0.174","S00017945":"0.099","S00017946":"0.141","S00017947":"0.175","S00017948":"0.169","S00017949":"0.203","S00017950":"0.179","S00017951":"0.160","S00017952":"0.148","S00017953":"0.151","S00017954":"0.162","S00017955":"0.157"},{"Metabolite":"fructose 1,6-bisphosphate","S00017942":"14.762","S00017943":"25.258","S00017944":"1.515","S00017945":"5.872","S00017946":"0.802","S00017947":"2.876","S00017948":"0.573","S00017949":"0.788","S00017950":"1.186","S00017951":"1.232","S00017952":"1.759","S00017953":"0.809","S00017954":"6.992","S00017955":"2.763"},{"Metabolite":"Fumaric acid","S00017942":"2.341","S00017943":"3.544","S00017944":"3.875","S00017945":"0.781","S00017946":"4.243","S00017947":"5.323","S00017948":"4.613","S00017949":"3.584","S00017950":"4.814","S00017951":"3.447","S00017952":"3.168","S00017953":"4.143","S00017954":"0.819","S00017955":"2.759"},{"Metabolite":"glucose 6-phosphate or fructose-6-phosphate","S00017942":"4.261","S00017943":"26.200","S00017944":"4.857","S00017945":"9.328","S00017946":"2.051","S00017947":"8.309","S00017948":"1.172","S00017949":"4.887","S00017950":"9.950","S00017951":"4.536","S00017952":"3.479","S00017953":"24.521","S00017954":"79.082","S00017955":"23.610"},{"Metabolite":"malate","S00017942":"5.604","S00017943":"6.244","S00017944":"6.617","S00017945":"6.528","S00017946":"7.596","S00017947":"8.942","S00017948":"9.771","S00017949":"7.650","S00017950":"8.614","S00017951":"6.655","S00017952":"6.159","S00017953":"7.666","S00017954":"9.289","S00017955":"8.712"},{"Metabolite":"nicotinamide adenine dinucleotide oxidized","S00017942":"2.600","S00017943":"2.471","S00017944":"0.196","S00017945":"1.332","S00017946":"0.553","S00017947":"0.111","S00017948":"0.236","S00017949":"0.345","S00017950":"0.214","S00017951":"0.709","S00017952":"0.233","S00017953":"0.369","S00017954":"0.098","S00017955":"0.315"},{"Metabolite":"nicotinamide adenine dinucleotide reduced","S00017942":"1.522","S00017943":"0.763","S00017944":"0.195","S00017945":"0.984","S00017946":"0.390","S00017947":"0.124","S00017948":"0.062","S00017949":"0.274","S00017950":"0.169","S00017951":"0.517","S00017952":"0.130","S00017953":"0.150","S00017954":"0.078","S00017955":"0.169"},{"Metabolite":"nicotinamide adenine dinucleotide phosphate oxidized","S00017942":"0.084","S00017943":"0.089","S00017944":"0.021","S00017945":"0.059","S00017946":"0.039","S00017947":"0.015","S00017948":"0.024","S00017949":"0.035","S00017950":"0.030","S00017951":"0.052","S00017952":"0.026","S00017953":"0.034","S00017954":"0.022","S00017955":"0.036"},{"Metabolite":"phosphoenolpyruvate","S00017942":"0.564","S00017943":"1.307","S00017944":"3.076","S00017945":"0.397","S00017946":"0.061","S00017947":"3.256","S00017948":"1.462","S00017949":"0.368","S00017950":"0.141","S00017951":"0.315","S00017952":"0.155","S00017953":"0.249","S00017954":"1.663","S00017955":"0.563"},{"Metabolite":"Pyruvic acid","S00017942":"46.614","S00017943":"44.378","S00017944":"35.248","S00017945":"","S00017946":"33.822","S00017947":"37.484","S00017948":"79.523","S00017949":"47.247","S00017950":"38.126","S00017951":"46.909","S00017952":"126.092","S00017953":"62.834","S00017954":"","S00017955":"43.445"},{"Metabolite":"ribose-5-phosphate or xylulose 5-phosphate","S00017942":"0.602","S00017943":"0.652","S00017944":"4.182","S00017945":"1.834","S00017946":"3.873","S00017947":"3.979","S00017948":"4.246","S00017949":"3.524","S00017950":"5.167","S00017951":"2.778","S00017952":"3.921","S00017953":"3.175","S00017954":"4.366","S00017955":"4.607"},{"Metabolite":"sedoheptulose 7-phosphate","S00017942":"0.064","S00017943":"0.050","S00017944":"0.025","S00017945":"0.034","S00017946":"0.043","S00017947":"0.020","S00017948":"0.037","S00017949":"0.020","S00017950":"0.111","S00017951":"0.032","S00017952":"0.037","S00017953":"0.092","S00017954":"0.170","S00017955":"0.065"}],

"Metabolites":[{"Metabolite":"2 or 3-phosphoglycerate","retention index":"","quantified m/z":"","PubChem ID":"724","KEGG ID":""},{"Metabolite":"6-phosphogluconate","retention index":"","quantified m/z":"","PubChem ID":"91493","KEGG ID":""},{"Metabolite":"acetyl-coa","retention index":"","quantified m/z":"","PubChem ID":"444493","KEGG ID":""},{"Metabolite":"adenosine diphosphate","retention index":"","quantified m/z":"","PubChem ID":"6022","KEGG ID":""},{"Metabolite":"Alpha-ketoglutaric acid","retention index":"","quantified m/z":"","PubChem ID":"51","KEGG ID":""},{"Metabolite":"adenosine monophosphate","retention index":"","quantified m/z":"","PubChem ID":"6083","KEGG ID":""},{"Metabolite":"adenosine triphosphate","retention index":"","quantified m/z":"","PubChem ID":"5957","KEGG ID":""},{"Metabolite":"citrate or isocitrate","retention index":"","quantified m/z":"","PubChem ID":"311","KEGG ID":""},{"Metabolite":"erythrose 4-phosphate","retention index":"","quantified m/z":"","PubChem ID":"122357","KEGG ID":""},{"Metabolite":"flavin adenine dinucleotide","retention index":"","quantified m/z":"","PubChem ID":"46906035","KEGG ID":""},{"Metabolite":"fructose 1,6-bisphosphate","retention index":"","quantified m/z":"","PubChem ID":"21125049","KEGG ID":""},{"Metabolite":"Fumaric acid","retention index":"","quantified m/z":"","PubChem ID":"444972","KEGG ID":""},{"Metabolite":"glucose 6-phosphate or fructose-6-phosphate","retention index":"","quantified m/z":"","PubChem ID":"5958","KEGG ID":""},{"Metabolite":"malate","retention index":"","quantified m/z":"","PubChem ID":"525","KEGG ID":""},{"Metabolite":"nicotinamide adenine dinucleotide oxidized","retention index":"","quantified m/z":"","PubChem ID":"15938971","KEGG ID":""},{"Metabolite":"nicotinamide adenine dinucleotide reduced","retention index":"","quantified m/z":"","PubChem ID":"439153","KEGG ID":""},{"Metabolite":"nicotinamide adenine dinucleotide phosphate oxidized","retention index":"","quantified m/z":"","PubChem ID":"15938972","KEGG ID":""},{"Metabolite":"phosphoenolpyruvate","retention index":"","quantified m/z":"","PubChem ID":"1005","KEGG ID":""},{"Metabolite":"Pyruvic acid","retention index":"","quantified m/z":"","PubChem ID":"1060","KEGG ID":""},{"Metabolite":"ribose-5-phosphate or xylulose 5-phosphate","retention index":"","quantified m/z":"","PubChem ID":"77982","KEGG ID":""},{"Metabolite":"sedoheptulose 7-phosphate","retention index":"","quantified m/z":"","PubChem ID":"165007","KEGG ID":""}]
}

}