{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST000459","ANALYSIS_ID":"AN000720","VERSION":"1","CREATED_ON":"September 8, 2016, 5:11 pm"},

"PROJECT":{"PROJECT_TITLE":"The effect of Odc knockout on amino acid homeostasis","PROJECT_TYPE":"Amino acid steady-state level analysis","PROJECT_SUMMARY":"YA95 is a lymphoma cell line from a Eμ-Myc;rtTA;Odc fl/fl mouse. The cell line was transduced with a Dox-inducible control vector (E) or a vector containing Cre recombinase (C). Doxycycline treatment promotes excision of Odc gene in YA95 C cells. In this experiment, we are ascertaining the effects of Odc deletion on amino acid homeostasis 48 hours after Dox treatment.","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 Odc knockout on amino acid steady state levels of Eμ-Myc lymphomas","STUDY_TYPE":"Cells are treated with vehicle or Doxycycline - to promote deletion of Odc gene","STUDY_SUMMARY":"Cells were collected 48 hours after treatment with Dox.","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":"4","TOTAL_SUBJECTS":"12","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","GENOTYPE_STRAIN":"Eμ-Myc;rtTA;Odc fl/fl - C57BL/6","CELL_STRAIN_DETAILS":"YA95","CELL_PRIMARY_IMMORTALIZED":"Immortalized","CELL_PASSAGE_NUMBER":"5","CELL_COUNTS":"6e6 to 20e6/sample"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"YA95 E",
"Sample ID":"YA95_1",
"Factors":{"Treatment":"Vehicle","Genotype":"Odc WT"},
"Additional sample data":{"Hours":"48"}
},
{
"Subject ID":"YA95 E",
"Sample ID":"YA95_2",
"Factors":{"Treatment":"Vehicle","Genotype":"Odc WT"},
"Additional sample data":{"Hours":"48"}
},
{
"Subject ID":"YA95 E",
"Sample ID":"YA95_3",
"Factors":{"Treatment":"Vehicle","Genotype":"Odc WT"},
"Additional sample data":{"Hours":"48"}
},
{
"Subject ID":"YA95 E",
"Sample ID":"YA95_4",
"Factors":{"Treatment":"Doxycycline","Genotype":"Odc WT"},
"Additional sample data":{"Hours":"48"}
},
{
"Subject ID":"YA95 E",
"Sample ID":"YA95_5",
"Factors":{"Treatment":"Doxycycline","Genotype":"Odc WT"},
"Additional sample data":{"Hours":"48"}
},
{
"Subject ID":"YA95 E",
"Sample ID":"YA95_6",
"Factors":{"Treatment":"Doxycycline","Genotype":"Odc WT"},
"Additional sample data":{"Hours":"48"}
},
{
"Subject ID":"YA95 C",
"Sample ID":"YA95_7",
"Factors":{"Treatment":"Vehicle","Genotype":"Odc WT"},
"Additional sample data":{"Hours":"48"}
},
{
"Subject ID":"YA95 C",
"Sample ID":"YA95_8",
"Factors":{"Treatment":"Vehicle","Genotype":"Odc WT"},
"Additional sample data":{"Hours":"48"}
},
{
"Subject ID":"YA95 C",
"Sample ID":"YA95_9",
"Factors":{"Treatment":"Vehicle","Genotype":"Odc WT"},
"Additional sample data":{"Hours":"48"}
},
{
"Subject ID":"YA95 C",
"Sample ID":"YA95_10",
"Factors":{"Treatment":"Doxycycline","Genotype":"Odc -/-"},
"Additional sample data":{"Hours":"48"}
},
{
"Subject ID":"YA95 C",
"Sample ID":"YA95_11",
"Factors":{"Treatment":"Doxycycline","Genotype":"Odc -/-"},
"Additional sample data":{"Hours":"48"}
},
{
"Subject ID":"YA95 C",
"Sample ID":"YA95_12",
"Factors":{"Treatment":"Doxycycline","Genotype":"Odc -/-"},
"Additional sample data":{"Hours":"48"}
}
],
"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":"Once at 48 hours post-treatment","VOLUMEORAMOUNT_COLLECTED":"Depends on sample. Collected as many cells as available. Total cell number range between samples is 6e6 to 20e6 cells per pellet","STORAGE_CONDITIONS":"Pellet","STORAGE_VIALS":"1.5 mL microfuge tube","TISSUE_CELL_IDENTIFICATION":"YA95"},

"TREATMENT":{"TREATMENT_SUMMARY":"Cells were treated with vehicle (dH2O) or 500 ng/mL doxycycline.","TREATMENT_COMPOUND":"Doxycycline","TREATMENT_DOSE":"500 ng/mL","TREATMENT_DOSEVOLUME":"4 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":{"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":"Alanine","YA95_1":"2.93","YA95_2":"4.30","YA95_3":"3.88","YA95_4":"4.38","YA95_5":"8.93","YA95_6":"7.05","YA95_7":"3.40","YA95_8":"4.24","YA95_9":"4.67","YA95_10":"4.63","YA95_11":"3.62","YA95_12":"4.25"},{"Metabolite":"Arginine","YA95_1":"0.06","YA95_2":"0.12","YA95_3":"0.07","YA95_4":"0.09","YA95_5":"0.10","YA95_6":"0.13","YA95_7":"0.06","YA95_8":"0.07","YA95_9":"0.09","YA95_10":"0.07","YA95_11":"0.16","YA95_12":"0.07"},{"Metabolite":"Asparagine","YA95_1":"0.07","YA95_2":"0.08","YA95_3":"0.07","YA95_4":"0.10","YA95_5":"0.11","YA95_6":"0.12","YA95_7":"0.06","YA95_8":"0.07","YA95_9":"0.10","YA95_10":"0.09","YA95_11":"0.14","YA95_12":"0.10"},{"Metabolite":"Aspartic Acid","YA95_1":"0.79","YA95_2":"0.62","YA95_3":"0.74","YA95_4":"0.76","YA95_5":"0.90","YA95_6":"1.11","YA95_7":"0.76","YA95_8":"0.66","YA95_9":"0.77","YA95_10":"0.88","YA95_11":"1.70","YA95_12":"0.90"},{"Metabolite":"Citrulline","YA95_1":"","YA95_2":"","YA95_3":"","YA95_4":"","YA95_5":"","YA95_6":"","YA95_7":"","YA95_8":"","YA95_9":"","YA95_10":"","YA95_11":"","YA95_12":""},{"Metabolite":"Glutamic Acid","YA95_1":"2.77","YA95_2":"4.31","YA95_3":"2.84","YA95_4":"3.46","YA95_5":"4.50","YA95_6":"7.09","YA95_7":"3.55","YA95_8":"3.57","YA95_9":"4.94","YA95_10":"3.86","YA95_11":"5.86","YA95_12":"3.59"},{"Metabolite":"Glutamine","YA95_1":"1.98","YA95_2":"2.37","YA95_3":"2.08","YA95_4":"2.22","YA95_5":"3.90","YA95_6":"4.21","YA95_7":"1.78","YA95_8":"1.99","YA95_9":"2.54","YA95_10":"2.39","YA95_11":"3.41","YA95_12":"2.79"},{"Metabolite":"Glycine","YA95_1":"1.35","YA95_2":"2.94","YA95_3":"2.30","YA95_4":"3.04","YA95_5":"3.25","YA95_6":"4.69","YA95_7":"2.56","YA95_8":"2.83","YA95_9":"2.61","YA95_10":"2.97","YA95_11":"2.45","YA95_12":"2.58"},{"Metabolite":"Histidine","YA95_1":"","YA95_2":"","YA95_3":"","YA95_4":"","YA95_5":"0.11","YA95_6":"0.15","YA95_7":"","YA95_8":"","YA95_9":"","YA95_10":"0.08","YA95_11":"0.13","YA95_12":"0.08"},{"Metabolite":"Isoleucine","YA95_1":"0.19","YA95_2":"0.23","YA95_3":"0.21","YA95_4":"0.22","YA95_5":"0.40","YA95_6":"0.37","YA95_7":"0.18","YA95_8":"0.19","YA95_9":"0.27","YA95_10":"0.25","YA95_11":"0.32","YA95_12":"0.25"},{"Metabolite":"Leucine","YA95_1":"0.16","YA95_2":"0.24","YA95_3":"0.20","YA95_4":"0.19","YA95_5":"0.36","YA95_6":"0.39","YA95_7":"0.14","YA95_8":"0.13","YA95_9":"0.23","YA95_10":"0.26","YA95_11":"0.38","YA95_12":"0.25"},{"Metabolite":"Lysine","YA95_1":"","YA95_2":"","YA95_3":"","YA95_4":"","YA95_5":"","YA95_6":"","YA95_7":"","YA95_8":"","YA95_9":"","YA95_10":"0.18","YA95_11":"0.17","YA95_12":""},{"Metabolite":"Ornithine","YA95_1":"","YA95_2":"","YA95_3":"","YA95_4":"","YA95_5":"","YA95_6":"","YA95_7":"","YA95_8":"","YA95_9":"","YA95_10":"0.04","YA95_11":"0.05","YA95_12":""},{"Metabolite":"Phenylalanine","YA95_1":"0.15","YA95_2":"0.19","YA95_3":"0.18","YA95_4":"0.24","YA95_5":"0.35","YA95_6":"0.27","YA95_7":"0.14","YA95_8":"0.16","YA95_9":"0.18","YA95_10":"0.16","YA95_11":"0.24","YA95_12":"0.17"},{"Metabolite":"Proline","YA95_1":"0.73","YA95_2":"0.92","YA95_3":"0.87","YA95_4":"0.94","YA95_5":"1.40","YA95_6":"1.71","YA95_7":"0.99","YA95_8":"0.63","YA95_9":"1.29","YA95_10":"0.63","YA95_11":"1.15","YA95_12":"0.76"},{"Metabolite":"Serine","YA95_1":"0.32","YA95_2":"0.50","YA95_3":"0.37","YA95_4":"0.36","YA95_5":"0.68","YA95_6":"0.77","YA95_7":"0.30","YA95_8":"0.38","YA95_9":"0.55","YA95_10":"0.45","YA95_11":"0.57","YA95_12":"0.44"},{"Metabolite":"Threonine","YA95_1":"1.10","YA95_2":"1.23","YA95_3":"1.49","YA95_4":"1.36","YA95_5":"1.51","YA95_6":"1.99","YA95_7":"1.09","YA95_8":"1.02","YA95_9":"1.34","YA95_10":"0.90","YA95_11":"1.62","YA95_12":"1.05"},{"Metabolite":"Tryptophan","YA95_1":"","YA95_2":"","YA95_3":"","YA95_4":"0.05","YA95_5":"0.06","YA95_6":"0.09","YA95_7":"","YA95_8":"0.05","YA95_9":"","YA95_10":"0.03","YA95_11":"0.05","YA95_12":"0.05"},{"Metabolite":"Tyrosine","YA95_1":"0.13","YA95_2":"0.10","YA95_3":"0.16","YA95_4":"0.19","YA95_5":"0.22","YA95_6":"0.33","YA95_7":"0.13","YA95_8":"0.16","YA95_9":"0.22","YA95_10":"0.15","YA95_11":"0.26","YA95_12":"0.20"},{"Metabolite":"Valine","YA95_1":"0.20","YA95_2":"0.29","YA95_3":"0.23","YA95_4":"0.26","YA95_5":"0.36","YA95_6":"0.52","YA95_7":"0.18","YA95_8":"0.22","YA95_9":"0.32","YA95_10":"0.23","YA95_11":"0.44","YA95_12":"0.26"}],

"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":"Aspartic Acid","retention index":"2.99","quantified m/z":"304.11","PubChem ID":"5960","KEGG ID":""},{"Metabolite":"Citrulline","retention index":"3.33","quantified m/z":"346.21","PubChem ID":"9750","KEGG ID":""},{"Metabolite":"Glutamic Acid","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":"Ornithine","retention index":"5.93","quantified m/z":"473.22","PubChem ID":"6262","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":""}]
}

}