{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST000499","ANALYSIS_ID":"AN000767","VERSION":"1","CREATED_ON":"October 31, 2016, 10:53 am"},

"PROJECT":{"PROJECT_TITLE":"The role of GBA1 in Parkinson's disease","PROJECT_SUMMARY":"The role of GBA1 in Parkinson's disease","INSTITUTE":"German Center for Neurodegenerative Diseases","DEPARTMENT":"Mitochondria and Inflammation in Neurodegeneration","LAST_NAME":"Deleidi","FIRST_NAME":"Michela","ADDRESS":"Otfried-Müller. Str 23, 72076, Tübingen, Germany","EMAIL":"michela.deleidi@dzne.de","PHONE":"none","FUNDING_SOURCE":"DFG"},

"STUDY":{"STUDY_TITLE":"NAD+ in neurodegeneration","STUDY_TYPE":"Baseline comparison of NAD metabolism in iPSC-derived neurons","STUDY_SUMMARY":"Differentiated iPSCs from patients and controls and knockout cells","INSTITUTE":"University of Florida","DEPARTMENT":"SECIM","LAST_NAME":"Deleidi","FIRST_NAME":"Michela","ADDRESS":"Otfried-Müller. Str 23, 72076, Tübingen, Germany","EMAIL":"michela.deleidi@dzne.de","PHONE":"none","NUM_GROUPS":"3","TOTAL_SUBJECTS":"17"},

"SUBJECT":{"SUBJECT_TYPE":"Cells","SUBJECT_SPECIES":"Homo sapiens","TAXONOMY_ID":"9606"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"105 PD1",
"Sample ID":"iPSC_01",
"Factors":{"Genotype":"WT/N370S"},
"Additional sample data":{"Gender":"male"}
},
{
"Subject ID":"105 PD1 GC",
"Sample ID":"iPSC_02",
"Factors":{"Genotype":"WT/WT"},
"Additional sample data":{"Gender":"male"}
},
{
"Subject ID":"105 PD1 KO1",
"Sample ID":"iPSC_03",
"Factors":{"Genotype":"KO/KO"},
"Additional sample data":{"Gender":"male"}
},
{
"Subject ID":"106 PD1",
"Sample ID":"iPSC_04",
"Factors":{"Genotype":"WT/N370S"},
"Additional sample data":{"Gender":"male"}
},
{
"Subject ID":"106 PD1 GC",
"Sample ID":"iPSC_05",
"Factors":{"Genotype":"WT/WT"},
"Additional sample data":{"Gender":"male"}
},
{
"Subject ID":"107 PD1",
"Sample ID":"iPSC_06",
"Factors":{"Genotype":"WT/N370S"},
"Additional sample data":{"Gender":"male"}
},
{
"Subject ID":"107 PD1 GC",
"Sample ID":"iPSC_07",
"Factors":{"Genotype":"WT/WT"},
"Additional sample data":{"Gender":"male"}
},
{
"Subject ID":"107 PD1 KO1",
"Sample ID":"iPSC_08",
"Factors":{"Genotype":"KO/KO"},
"Additional sample data":{"Gender":"male"}
},
{
"Subject ID":"107 PD1 KO2",
"Sample ID":"iPSC_09",
"Factors":{"Genotype":"KO/KO"},
"Additional sample data":{"Gender":"male"}
},
{
"Subject ID":"108 PD1",
"Sample ID":"iPSC_10",
"Factors":{"Genotype":"WT/N370S"},
"Additional sample data":{"Gender":"male"}
},
{
"Subject ID":"108 PD1 GC",
"Sample ID":"iPSC_11",
"Factors":{"Genotype":"WT/WT"},
"Additional sample data":{"Gender":"male"}
},
{
"Subject ID":"109 PD1",
"Sample ID":"iPSC_12",
"Factors":{"Genotype":"WT/N370S"},
"Additional sample data":{"Gender":"male"}
},
{
"Subject ID":"109 PD1 GC",
"Sample ID":"iPSC_13",
"Factors":{"Genotype":"WT/WT"},
"Additional sample data":{"Gender":"male"}
},
{
"Subject ID":"110 PD2",
"Sample ID":"iPSC_14",
"Factors":{"Genotype":"WT/L444P"},
"Additional sample data":{"Gender":"male"}
},
{
"Subject ID":"110 PD2 GC",
"Sample ID":"iPSC_15",
"Factors":{"Genotype":"WT/WT"},
"Additional sample data":{"Gender":"male"}
},
{
"Subject ID":"111 PD2",
"Sample ID":"iPSC_16",
"Factors":{"Genotype":"WT/L444P"},
"Additional sample data":{"Gender":"male"}
},
{
"Subject ID":"111 PD2 GC",
"Sample ID":"iPSC_17",
"Factors":{"Genotype":"WT/WT"},
"Additional sample data":{"Gender":"male"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"Cells were washed once with cold PBS, scraped off the plate in 1 ml cold PBS, transfered in pre-cooled 50 ml falcons and pelleted by centrifugation 3000rpm at 4°C. PBS was taken off and pellets were then snap frozen in liquid N2 and stored at -80°C."},

"TREATMENT":{"TREATMENT_SUMMARY":"80% confluence, 48 hrs after last media change, differentiation medium (Neurobasal/B27/L-glut containing medium supplemented with BDNF, ascorbic acid , GDNF, TGFβ3, dibutyryl cAMP and DAPT."},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"none","SAMPLEPREP_PROTOCOL_FILENAME":"SB_NAD-ATP_Assay_Agilent.pdf"},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_TYPE":"Reversed phase","INSTRUMENT_NAME":"Agilent 1290 Infinity","COLUMN_NAME":"Thermo Hypercarb (50 x 2.1mm, 3um)","METHODS_FILENAME":"SB_NAD-ATP_Assay_Agilent.pdf"},

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

"MS":{"MS_COMMENTS":"-","INSTRUMENT_NAME":"Agilent 6490 QQQ","INSTRUMENT_TYPE":"Triple quadrupole","MS_TYPE":"ESI","ION_MODE":"POSITIVE"},

"MS_METABOLITE_DATA":{
"Units":"nmol/mg protein",

"Data":[{"Metabolite":"1-Methyl NAM","iPSC_01":"","iPSC_02":"","iPSC_03":"","iPSC_04":"","iPSC_05":"","iPSC_06":"ND","iPSC_07":"","iPSC_08":"","iPSC_09":"0.64","iPSC_10":"","iPSC_11":"","iPSC_12":"","iPSC_13":"","iPSC_14":"","iPSC_15":"0.54","iPSC_16":"","iPSC_17":""},{"Metabolite":"NAM","iPSC_01":"0.73","iPSC_02":"","iPSC_03":"","iPSC_04":"1.20","iPSC_05":"0.63","iPSC_06":"0.69","iPSC_07":"0.68","iPSC_08":"0.95","iPSC_09":"1.29","iPSC_10":"0.87","iPSC_11":"0.60","iPSC_12":"1.08","iPSC_13":"1.01","iPSC_14":"2.43","iPSC_15":"0.96","iPSC_16":"0.66","iPSC_17":""},{"Metabolite":"NMN","iPSC_01":"ND","iPSC_02":"ND","iPSC_03":"ND","iPSC_04":"ND","iPSC_05":"ND","iPSC_06":"ND","iPSC_07":"ND","iPSC_08":"ND","iPSC_09":"ND","iPSC_10":"ND","iPSC_11":"ND","iPSC_12":"ND","iPSC_13":"ND","iPSC_14":"ND","iPSC_15":"ND","iPSC_16":"ND","iPSC_17":"ND"},{"Metabolite":"NAD","iPSC_01":"2.55","iPSC_02":"","iPSC_03":"2.74","iPSC_04":"4.72","iPSC_05":"1.59","iPSC_06":"1.90","iPSC_07":"2.60","iPSC_08":"2.22","iPSC_09":"3.51","iPSC_10":"1.96","iPSC_11":"0.98","iPSC_12":"2.21","iPSC_13":"2.07","iPSC_14":"3.70","iPSC_15":"2.32","iPSC_16":"1.77","iPSC_17":"1.60"},{"Metabolite":"NADP","iPSC_01":"","iPSC_02":"","iPSC_03":"","iPSC_04":"","iPSC_05":"","iPSC_06":"","iPSC_07":"","iPSC_08":"","iPSC_09":"","iPSC_10":"","iPSC_11":"","iPSC_12":"","iPSC_13":"","iPSC_14":"","iPSC_15":"","iPSC_16":"","iPSC_17":""},{"Metabolite":"NADH","iPSC_01":"0.56","iPSC_02":"0.07","iPSC_03":"","iPSC_04":"0.28","iPSC_05":"0.10","iPSC_06":"0.39","iPSC_07":"0.22","iPSC_08":"0.48","iPSC_09":"0.34","iPSC_10":"0.23","iPSC_11":"0.34","iPSC_12":"0.18","iPSC_13":"0.25","iPSC_14":"0.13","iPSC_15":"0.45","iPSC_16":"0.22","iPSC_17":"0.16"},{"Metabolite":"NADPH","iPSC_01":"0.50","iPSC_02":"0.07","iPSC_03":"0.12","iPSC_04":"0.17","iPSC_05":"0.07","iPSC_06":"0.37","iPSC_07":"0.34","iPSC_08":"0.19","iPSC_09":"0.36","iPSC_10":"0.28","iPSC_11":"0.29","iPSC_12":"0.26","iPSC_13":"0.32","iPSC_14":"0.23","iPSC_15":"0.54","iPSC_16":"0.37","iPSC_17":"0.38"},{"Metabolite":"AMP","iPSC_01":"","iPSC_02":"","iPSC_03":"","iPSC_04":"","iPSC_05":"1.99","iPSC_06":"","iPSC_07":"5.16","iPSC_08":"6.24","iPSC_09":"4.27","iPSC_10":"3.77","iPSC_11":"8.33","iPSC_12":"4.14","iPSC_13":"13.34","iPSC_14":"7.78","iPSC_15":"","iPSC_16":"3.88","iPSC_17":"11.64"},{"Metabolite":"ADP","iPSC_01":"6.78","iPSC_02":"18.66","iPSC_03":"5.35","iPSC_04":"9.53","iPSC_05":"5.74","iPSC_06":"6.38","iPSC_07":"9.63","iPSC_08":"9.98","iPSC_09":"13.53","iPSC_10":"9.46","iPSC_11":"4.92","iPSC_12":"10.57","iPSC_13":"10.72","iPSC_14":"22.21","iPSC_15":"10.42","iPSC_16":"9.38","iPSC_17":"5.06"},{"Metabolite":"ATP","iPSC_01":"19.30","iPSC_02":"32.14","iPSC_03":"21.20","iPSC_04":"29.31","iPSC_05":"7.96","iPSC_06":"16.49","iPSC_07":"10.65","iPSC_08":"10.35","iPSC_09":"25.73","iPSC_10":"14.30","iPSC_11":"2.80","iPSC_12":"16.22","iPSC_13":"6.17","iPSC_14":"42.30","iPSC_15":"26.10","iPSC_16":"14.28","iPSC_17":""},{"Metabolite":"GDP","iPSC_01":"1.62","iPSC_02":"5.02","iPSC_03":"1.48","iPSC_04":"2.33","iPSC_05":"1.55","iPSC_06":"1.46","iPSC_07":"2.29","iPSC_08":"2.45","iPSC_09":"2.95","iPSC_10":"2.21","iPSC_11":"1.53","iPSC_12":"2.53","iPSC_13":"3.04","iPSC_14":"4.76","iPSC_15":"2.16","iPSC_16":"1.99","iPSC_17":"2.41"},{"Metabolite":"GTP","iPSC_01":"3.97","iPSC_02":"8.92","iPSC_03":"4.33","iPSC_04":"6.20","iPSC_05":"2.10","iPSC_06":"3.38","iPSC_07":"2.67","iPSC_08":"2.49","iPSC_09":"4.79","iPSC_10":"3.19","iPSC_11":"1.09","iPSC_12":"3.63","iPSC_13":"2.07","iPSC_14":"9.02","iPSC_15":"5.29","iPSC_16":"3.15","iPSC_17":"1.40"},{"Metabolite":"CDP","iPSC_01":"0.53","iPSC_02":"","iPSC_03":"","iPSC_04":"0.55","iPSC_05":"","iPSC_06":"","iPSC_07":"","iPSC_08":"0.59","iPSC_09":"0.55","iPSC_10":"","iPSC_11":"","iPSC_12":"0.75","iPSC_13":"","iPSC_14":"1.73","iPSC_15":"0.78","iPSC_16":"0.60","iPSC_17":""},{"Metabolite":"CTP","iPSC_01":"1.79","iPSC_02":"3.31","iPSC_03":"2.08","iPSC_04":"2.76","iPSC_05":"0.52","iPSC_06":"1.36","iPSC_07":"0.83","iPSC_08":"0.78","iPSC_09":"1.62","iPSC_10":"1.21","iPSC_11":"","iPSC_12":"1.50","iPSC_13":"","iPSC_14":"4.42","iPSC_15":"2.66","iPSC_16":"1.20","iPSC_17":""},{"Metabolite":"UDP","iPSC_01":"1.26","iPSC_02":"","iPSC_03":"1.18","iPSC_04":"1.63","iPSC_05":"0.92","iPSC_06":"1.05","iPSC_07":"1.50","iPSC_08":"1.74","iPSC_09":"2.50","iPSC_10":"1.68","iPSC_11":"1.22","iPSC_12":"1.94","iPSC_13":"2.06","iPSC_14":"5.25","iPSC_15":"2.15","iPSC_16":"1.58","iPSC_17":"1.08"},{"Metabolite":"UTP","iPSC_01":"6.38","iPSC_02":"8.60","iPSC_03":"7.25","iPSC_04":"9.98","iPSC_05":"2.22","iPSC_06":"5.13","iPSC_07":"2.96","iPSC_08":"2.98","iPSC_09":"7.93","iPSC_10":"4.49","iPSC_11":"0.91","iPSC_12":"5.34","iPSC_13":"2.09","iPSC_14":"18.78","iPSC_15":"10.37","iPSC_16":"4.74","iPSC_17":""}],

"Metabolites":[{"Metabolite":"NMN","retention index":"1.13","quantified m/z":"335.2, 123.1","PubChem ID":"14180","KEGG ID":""},{"Metabolite":"NAD","retention index":"1.80","quantified m/z":"664.2, 136.1","PubChem ID":"5893","KEGG ID":""},{"Metabolite":"NADP","retention index":"1.64","quantified m/z":"744.2, 136.1","PubChem ID":"5886","KEGG ID":""},{"Metabolite":"NADH","retention index":"1.86","quantified m/z":"666.2, 649.2","PubChem ID":"439153","KEGG ID":""},{"Metabolite":"NADPH","retention index":"0.66","quantified m/z":"746.2, 729.2","PubChem ID":"5884","KEGG ID":""},{"Metabolite":"AMP","retention index":"1.51","quantified m/z":"348.1, 136.1","PubChem ID":"6083","KEGG ID":""},{"Metabolite":"ADP","retention index":"1.51","quantified m/z":"428.0, 136.1","PubChem ID":"6022","KEGG ID":""},{"Metabolite":"ATP","retention index":"1.50","quantified m/z":"508.1, 136.1","PubChem ID":"5957","KEGG ID":""},{"Metabolite":"1-Methyl NAM","retention index":"","quantified m/z":"","PubChem ID":"","KEGG ID":""},{"Metabolite":"NAM","retention index":"","quantified m/z":"","PubChem ID":"","KEGG ID":""},{"Metabolite":"GDP","retention index":"","quantified m/z":"","PubChem ID":"","KEGG ID":""},{"Metabolite":"GTP","retention index":"","quantified m/z":"","PubChem ID":"","KEGG ID":""},{"Metabolite":"CDP","retention index":"","quantified m/z":"","PubChem ID":"","KEGG ID":""},{"Metabolite":"CTP","retention index":"","quantified m/z":"","PubChem ID":"","KEGG ID":""},{"Metabolite":"UDP","retention index":"","quantified m/z":"","PubChem ID":"","KEGG ID":""},{"Metabolite":"UTP","retention index":"","quantified m/z":"","PubChem ID":"","KEGG ID":""}]
}

}