{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST000460","ANALYSIS_ID":"AN000721","VERSION":"1","CREATED_ON":"September 8, 2016, 5:22 pm"},

"PROJECT":{"PROJECT_TITLE":"Effect of ATG7 reconstitution in AGY571 cells","PROJECT_TYPE":"Amino acid steady-state level analysis","PROJECT_SUMMARY":"AGY571 is a B cell lymphoma isolated from Eu-Myc CD19-Cre;ATG7fl/fl mice. AGY571 cells engineered to express rtTA and Dox-inducible GFP or ATG7 were treated with 500 ng/mL or 1 ug/mL Doxycycline for 48 hours. Assessing the effects of ATG7 reexpression in B cell lymphoma.","INSTITUTE":"H. Lee Moffitt Cancer Center","DEPARTMENT":"Tumor Biology","LABORATORY":"John Cleveland","LAST_NAME":"Fernandez","FIRST_NAME":"Mario","ADDRESS":"12902 Magnolia Drive, MRC 4-West","EMAIL":"mario.fernandez@moffitt.org","PHONE":"813-745-5140","FUNDING_SOURCE":"5R01CA154739"},

"STUDY":{"STUDY_TITLE":"Effect of ATG7 reconstitution in AGY571 cells","STUDY_TYPE":"Cells are treated with vehicle or Doxycycline - to induce expression of GFP or ATG7","STUDY_SUMMARY":"AGY571 cells engineered to express Dox-inducible GFP or ATG7 were treated with 500 ng/mL or 1 ug/mL Doxycycline for 48 hours. Assessing the effects of ATG7 reexpression in B cell lymphoma.","INSTITUTE":"University of Florida","DEPARTMENT":"SECIM","LABORATORY":"John Cleveland","LAST_NAME":"Fernandez","FIRST_NAME":"Mario","ADDRESS":"12902 Magnolia Drive, MRC 4-West","EMAIL":"mario.fernandez@moffitt.org","PHONE":"813-745-5140","NUM_GROUPS":"5","TOTAL_SUBJECTS":"15","STUDY_COMMENTS":"Groups collected in triplicate per time point, either treated or untreated with Doxycycline."},

"SUBJECT":{"SUBJECT_TYPE":"Cells","SUBJECT_SPECIES":"Mus musculus","TAXONOMY_ID":"10090","CELL_STRAIN_DETAILS":"AGY571","SUBJECT_COMMENTS":"See study design section for cell number per sample for cell counts","CELL_PRIMARY_IMMORTALIZED":"Immortalized"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"AGY571_GFP",
"Sample ID":"AGY571_001",
"Factors":{"Treatment":"Doxycycline","Dox Concentration":"1 ug/mL","Ectopic Gene Expression":"GFP (ATG7-/-)"},
"Additional sample data":{"Hours":"48","Genotype":"Eu-Myc ATG7-/-","Cell Count (in millions)":"9"}
},
{
"Subject ID":"AGY571_GFP",
"Sample ID":"AGY571_002",
"Factors":{"Treatment":"Doxycycline","Dox Concentration":"1 ug/mL","Ectopic Gene Expression":"GFP (ATG7-/-)"},
"Additional sample data":{"Hours":"48","Genotype":"Eu-Myc ATG7-/-","Cell Count (in millions)":"9.36"}
},
{
"Subject ID":"AGY571_GFP",
"Sample ID":"AGY571_003",
"Factors":{"Treatment":"Doxycycline","Dox Concentration":"1 ug/mL","Ectopic Gene Expression":"GFP (ATG7-/-)"},
"Additional sample data":{"Hours":"48","Genotype":"Eu-Myc ATG7-/-","Cell Count (in millions)":"6.705"}
},
{
"Subject ID":"AGY571_ATG7",
"Sample ID":"AGY571_004",
"Factors":{"Treatment":"Vehicle","Dox Concentration":"0 ug/mL","Ectopic Gene Expression":"None (ATG7-/- backgound)"},
"Additional sample data":{"Hours":"48","Genotype":"Eu-Myc ATG7-/-","Cell Count (in millions)":"8.91"}
},
{
"Subject ID":"AGY571_ATG7",
"Sample ID":"AGY571_005",
"Factors":{"Treatment":"Vehicle","Dox Concentration":"0 ug/mL","Ectopic Gene Expression":"None (ATG7-/- backgound)"},
"Additional sample data":{"Hours":"48","Genotype":"Eu-Myc ATG7-/-","Cell Count (in millions)":"4.725"}
},
{
"Subject ID":"AGY571_ATG7",
"Sample ID":"AGY571_006",
"Factors":{"Treatment":"Vehicle","Dox Concentration":"0 ug/mL","Ectopic Gene Expression":"None (ATG7-/- backgound)"},
"Additional sample data":{"Hours":"48","Genotype":"Eu-Myc ATG7-/-","Cell Count (in millions)":"7.74"}
},
{
"Subject ID":"AGY571_ATG7",
"Sample ID":"AGY571_007",
"Factors":{"Treatment":"Doxycycline","Dox Concentration":"1 ug/mL","Ectopic Gene Expression":"ATG7"},
"Additional sample data":{"Hours":"48","Genotype":"Eu-Myc ATG7-/-","Cell Count (in millions)":"7.74"}
},
{
"Subject ID":"AGY571_ATG7",
"Sample ID":"AGY571_008",
"Factors":{"Treatment":"Doxycycline","Dox Concentration":"1 ug/mL","Ectopic Gene Expression":"ATG7"},
"Additional sample data":{"Hours":"48","Genotype":"Eu-Myc ATG7-/-","Cell Count (in millions)":"4.68"}
},
{
"Subject ID":"AGY571_ATG7",
"Sample ID":"AGY571_009",
"Factors":{"Treatment":"Doxycycline","Dox Concentration":"1 ug/mL","Ectopic Gene Expression":"ATG7"},
"Additional sample data":{"Hours":"48","Genotype":"Eu-Myc ATG7-/-","Cell Count (in millions)":"5.31"}
},
{
"Subject ID":"AGY571_GFP",
"Sample ID":"AGY571_010",
"Factors":{"Treatment":"Doxycycline","Dox Concentration":"500 ng/mL","Ectopic Gene Expression":"GFP (ATG7-/-)"},
"Additional sample data":{"Hours":"48","Genotype":"Eu-Myc ATG7-/-","Cell Count (in millions)":"7.584"}
},
{
"Subject ID":"AGY571_GFP",
"Sample ID":"AGY571_011",
"Factors":{"Treatment":"Doxycycline","Dox Concentration":"500 ng/mL","Ectopic Gene Expression":"GFP (ATG7-/-)"},
"Additional sample data":{"Hours":"48","Genotype":"Eu-Myc ATG7-/-","Cell Count (in millions)":"7.056"}
},
{
"Subject ID":"AGY571_GFP",
"Sample ID":"AGY571_012",
"Factors":{"Treatment":"Doxycycline","Dox Concentration":"500 ng/mL","Ectopic Gene Expression":"GFP (ATG7-/-)"},
"Additional sample data":{"Hours":"48","Genotype":"Eu-Myc ATG7-/-","Cell Count (in millions)":"5.16"}
},
{
"Subject ID":"AGY571_ATG7",
"Sample ID":"AGY571_013",
"Factors":{"Treatment":"Doxycycline","Dox Concentration":"500 ng/mL","Ectopic Gene Expression":"ATG7"},
"Additional sample data":{"Hours":"48","Genotype":"Eu-Myc ATG7-/-","Cell Count (in millions)":"8.496"}
},
{
"Subject ID":"AGY571_ATG7",
"Sample ID":"AGY571_014",
"Factors":{"Treatment":"Doxycycline","Dox Concentration":"500 ng/mL","Ectopic Gene Expression":"ATG7"},
"Additional sample data":{"Hours":"48","Genotype":"Eu-Myc ATG7-/-","Cell Count (in millions)":"7.728"}
},
{
"Subject ID":"AGY571_ATG7",
"Sample ID":"AGY571_015",
"Factors":{"Treatment":"Doxycycline","Dox Concentration":"500 ng/mL","Ectopic Gene Expression":"ATG7"},
"Additional sample data":{"Hours":"48","Genotype":"Eu-Myc ATG7-/-","Cell Count (in millions)":"9.264"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"Cells were counted, cells were collected via centrifugation, washed twice with cold 1x PBS, PBS removed and flash frozen. Pellets were saved at -80 C.","SAMPLE_TYPE":"Cell","COLLECTION_METHOD":"Pellet","COLLECTION_LOCATION":"Lab","COLLECTION_FREQUENCY":"48 hours after Dox treatment","STORAGE_CONDITIONS":"Pellet at -80C","STORAGE_VIALS":"1.5 mL microfuge tube","TISSUE_CELL_IDENTIFICATION":"AGY571 cells"},

"TREATMENT":{"TREATMENT_SUMMARY":"Cells were treated with vehicle (dH2O) or 500 ng/mL doxycycline.","TREATMENT_COMPOUND":"Doxycycline","TREATMENT_DOSE":"0.5-1.0 ug/mL","TREATMENT_DOSEVOLUME":"5 mL","TREATMENT_DOSEDURATION":"48 hours","TREATMENT_VEHICLE":"dH2O","CELL_GROWTH_CONTAINER":"6-well plate"},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"Amino acid","SAMPLEPREP_PROTOCOL_FILENAME":"SB_AA_Assay.pdf"},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_SUMMARY":"Amino Acid","CHROMATOGRAPHY_TYPE":"Reversed phase","INSTRUMENT_NAME":"Agilent 1290 Infinity","COLUMN_NAME":"Waters AccQ Tag (100 x 2mm, 1.7um)","METHODS_FILENAME":"SB_AA_Assay.pdf"},

"ANALYSIS":{"ANALYSIS_TYPE":"MS","LABORATORY_NAME":"Sanford Burnham"},

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

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

"Data":[{"Metabolite":"Alanine","AGY571_004":"1.49","AGY571_005":"3.07","AGY571_006":"1.95","AGY571_001":"1.45","AGY571_002":"1.53","AGY571_003":"1.76","AGY571_010":"1.27","AGY571_011":"1.26","AGY571_012":"1.66","AGY571_007":"1.44","AGY571_008":"2.30","AGY571_009":"2.42","AGY571_013":"1.42","AGY571_014":"1.65","AGY571_015":"1.76"},{"Metabolite":"Arginine","AGY571_004":"0.10","AGY571_005":"0.18","AGY571_006":"0.15","AGY571_001":"0.12","AGY571_002":"0.08","AGY571_003":"0.10","AGY571_010":"0.06","AGY571_011":"0.10","AGY571_012":"0.12","AGY571_007":"0.09","AGY571_008":"0.18","AGY571_009":"0.17","AGY571_013":"0.09","AGY571_014":"0.10","AGY571_015":"0.08"},{"Metabolite":"Asparagine","AGY571_004":"0.12","AGY571_005":"0.24","AGY571_006":"0.14","AGY571_001":"0.12","AGY571_002":"0.10","AGY571_003":"0.17","AGY571_010":"0.11","AGY571_011":"0.12","AGY571_012":"0.15","AGY571_007":"0.10","AGY571_008":"0.18","AGY571_009":"0.18","AGY571_013":"0.10","AGY571_014":"0.11","AGY571_015":"0.10"},{"Metabolite":"Aspartate","AGY571_004":"0.52","AGY571_005":"1.03","AGY571_006":"0.60","AGY571_001":"0.64","AGY571_002":"0.47","AGY571_003":"0.78","AGY571_010":"1.22","AGY571_011":"1.15","AGY571_012":"1.61","AGY571_007":"0.54","AGY571_008":"0.93","AGY571_009":"0.91","AGY571_013":"0.65","AGY571_014":"0.86","AGY571_015":"0.77"},{"Metabolite":"Glutamate","AGY571_004":"4.62","AGY571_005":"9.31","AGY571_006":"5.55","AGY571_001":"4.18","AGY571_002":"4.36","AGY571_003":"5.80","AGY571_010":"4.91","AGY571_011":"6.32","AGY571_012":"7.98","AGY571_007":"4.96","AGY571_008":"9.86","AGY571_009":"8.52","AGY571_013":"4.64","AGY571_014":"5.79","AGY571_015":"5.78"},{"Metabolite":"Glutamine","AGY571_004":"3.76","AGY571_005":"8.56","AGY571_006":"6.03","AGY571_001":"4.60","AGY571_002":"4.20","AGY571_003":"5.85","AGY571_010":"5.19","AGY571_011":"5.72","AGY571_012":"7.48","AGY571_007":"4.51","AGY571_008":"5.96","AGY571_009":"7.83","AGY571_013":"4.41","AGY571_014":"4.44","AGY571_015":"4.69"},{"Metabolite":"Glycine","AGY571_004":"1.22","AGY571_005":"2.41","AGY571_006":"1.43","AGY571_001":"1.07","AGY571_002":"0.99","AGY571_003":"1.63","AGY571_010":"1.07","AGY571_011":"1.04","AGY571_012":"1.99","AGY571_007":"1.38","AGY571_008":"1.94","AGY571_009":"2.27","AGY571_013":"1.18","AGY571_014":"1.53","AGY571_015":"1.33"},{"Metabolite":"Histidine","AGY571_004":"0.04","AGY571_005":"0.11","AGY571_006":"0.08","AGY571_001":"0.05","AGY571_002":"0.07","AGY571_003":"0.09","AGY571_010":"0.06","AGY571_011":"0.06","AGY571_012":"0.11","AGY571_007":"0.04","AGY571_008":"0.07","AGY571_009":"0.10","AGY571_013":"0.06","AGY571_014":"0.07","AGY571_015":"0.07"},{"Metabolite":"Isoleucine","AGY571_004":"0.09","AGY571_005":"0.25","AGY571_006":"0.22","AGY571_001":"0.13","AGY571_002":"0.16","AGY571_003":"0.25","AGY571_010":"0.17","AGY571_011":"0.17","AGY571_012":"0.23","AGY571_007":"0.11","AGY571_008":"0.15","AGY571_009":"0.29","AGY571_013":"0.17","AGY571_014":"0.15","AGY571_015":"0.20"},{"Metabolite":"Leucine","AGY571_004":"0.11","AGY571_005":"0.29","AGY571_006":"0.19","AGY571_001":"0.14","AGY571_002":"0.16","AGY571_003":"0.22","AGY571_010":"0.14","AGY571_011":"0.17","AGY571_012":"0.25","AGY571_007":"0.12","AGY571_008":"0.18","AGY571_009":"0.23","AGY571_013":"0.15","AGY571_014":"0.17","AGY571_015":"0.18"},{"Metabolite":"Lysine","AGY571_004":"","AGY571_005":"0.46","AGY571_006":"0.27","AGY571_001":"0.19","AGY571_002":"0.20","AGY571_003":"0.33","AGY571_010":"","AGY571_011":"","AGY571_012":"","AGY571_007":"","AGY571_008":"","AGY571_009":"0.34","AGY571_013":"","AGY571_014":"0.21","AGY571_015":""},{"Metabolite":"Phenylalanine","AGY571_004":"0.07","AGY571_005":"0.22","AGY571_006":"0.17","AGY571_001":"0.08","AGY571_002":"0.12","AGY571_003":"0.15","AGY571_010":"0.09","AGY571_011":"0.11","AGY571_012":"0.17","AGY571_007":"0.08","AGY571_008":"0.14","AGY571_009":"0.17","AGY571_013":"0.12","AGY571_014":"0.13","AGY571_015":"0.16"},{"Metabolite":"Proline","AGY571_004":"1.08","AGY571_005":"1.94","AGY571_006":"1.08","AGY571_001":"0.88","AGY571_002":"0.86","AGY571_003":"1.21","AGY571_010":"0.63","AGY571_011":"0.75","AGY571_012":"0.98","AGY571_007":"0.96","AGY571_008":"1.46","AGY571_009":"1.78","AGY571_013":"0.80","AGY571_014":"0.90","AGY571_015":"0.78"},{"Metabolite":"Serine","AGY571_004":"0.32","AGY571_005":"0.54","AGY571_006":"0.33","AGY571_001":"0.35","AGY571_002":"0.33","AGY571_003":"0.51","AGY571_010":"0.27","AGY571_011":"0.37","AGY571_012":"0.64","AGY571_007":"0.39","AGY571_008":"0.54","AGY571_009":"0.58","AGY571_013":"0.30","AGY571_014":"0.37","AGY571_015":"0.37"},{"Metabolite":"Threonine","AGY571_004":"0.87","AGY571_005":"1.82","AGY571_006":"1.05","AGY571_001":"0.90","AGY571_002":"0.82","AGY571_003":"0.84","AGY571_010":"0.86","AGY571_011":"0.91","AGY571_012":"1.26","AGY571_007":"0.85","AGY571_008":"1.52","AGY571_009":"1.60","AGY571_013":"0.82","AGY571_014":"0.94","AGY571_015":"0.77"},{"Metabolite":"Tryptophan","AGY571_004":"0.03","AGY571_005":"0.04","AGY571_006":"0.04","AGY571_001":"0.03","AGY571_002":"0.03","AGY571_003":"0.05","AGY571_010":"0.03","AGY571_011":"0.03","AGY571_012":"0.04","AGY571_007":"0.03","AGY571_008":"0.04","AGY571_009":"0.05","AGY571_013":"0.04","AGY571_014":"0.03","AGY571_015":"0.03"},{"Metabolite":"Tyrosine","AGY571_004":"0.10","AGY571_005":"0.32","AGY571_006":"0.20","AGY571_001":"0.14","AGY571_002":"0.17","AGY571_003":"0.22","AGY571_010":"0.14","AGY571_011":"0.17","AGY571_012":"0.27","AGY571_007":"0.12","AGY571_008":"0.18","AGY571_009":"0.25","AGY571_013":"0.16","AGY571_014":"0.18","AGY571_015":"0.17"},{"Metabolite":"Valine","AGY571_004":"","AGY571_005":"0.39","AGY571_006":"0.28","AGY571_001":"0.18","AGY571_002":"0.22","AGY571_003":"0.30","AGY571_010":"0.21","AGY571_011":"","AGY571_012":"0.29","AGY571_007":"","AGY571_008":"","AGY571_009":"0.36","AGY571_013":"0.22","AGY571_014":"0.23","AGY571_015":"0.23"}],

"Metabolites":[{"Metabolite":"Alanine","retention index":"4.16","quantified m/z":"260.17","PubChem ID":"5950","KEGG ID":""},{"Metabolite":"Arginine","retention index":"2.68","quantified m/z":"345.21","PubChem ID":"6322","KEGG ID":""},{"Metabolite":"Asparagine","retention index":"2.25","quantified m/z":"303.13","PubChem ID":"6267","KEGG ID":""},{"Metabolite":"Aspartate","retention index":"2.99","quantified m/z":"304.11","PubChem ID":"5960","KEGG ID":""},{"Metabolite":"Glutamate","retention index":"3.35","quantified m/z":"318.11","PubChem ID":"33032","KEGG ID":""},{"Metabolite":"Glutamine","retention index":"2.65","quantified m/z":"317.21","PubChem ID":"5961","KEGG ID":""},{"Metabolite":"Glycine","retention index":"2.81","quantified m/z":"246.08","PubChem ID":"750","KEGG ID":""},{"Metabolite":"Histidine","retention index":"2.07","quantified m/z":"326.21","PubChem ID":"6274","KEGG ID":""},{"Metabolite":"Isoleucine","retention index":"8.15","quantified m/z":"302.21","PubChem ID":"6306","KEGG ID":""},{"Metabolite":"Leucine","retention index":"8.26","quantified m/z":"302.21","PubChem ID":"6106","KEGG ID":""},{"Metabolite":"Lysine","retention index":"6.66","quantified m/z":"487.21","PubChem ID":"5962","KEGG ID":""},{"Metabolite":"Phenylalanine","retention index":"8.40","quantified m/z":"336.21","PubChem ID":"6140","KEGG ID":""},{"Metabolite":"Proline","retention index":"4.84","quantified m/z":"286.16","PubChem ID":"145742","KEGG ID":""},{"Metabolite":"Serine","retention index":"2.60","quantified m/z":"276.11","PubChem ID":"5951","KEGG ID":""},{"Metabolite":"Threonine","retention index":"3.74","quantified m/z":"290.11","PubChem ID":"6288","KEGG ID":""},{"Metabolite":"Tryptophan","retention index":"8.54","quantified m/z":"375.21","PubChem ID":"6305","KEGG ID":""},{"Metabolite":"Tyrosine","retention index":"6.66","quantified m/z":"352.21","PubChem ID":"6057","KEGG ID":""},{"Metabolite":"Valine","retention index":"7.09","quantified m/z":"288.21","PubChem ID":"6287","KEGG ID":""}]
}

}