{
"METABOLOMICS WORKBENCH":{"VERSION":"1","CREATED_ON":"November 17, 2016, 3:26 pm"},

"PROJECT":{"PROJECT_TITLE":"Effect of Odc knockout on amino acid homeostasis of Eu-Myc Lymphomas","PROJECT_TYPE":"Amino acid steady-state level analysis","PROJECT_SUMMARY":"Analysis of two B cell lymphomas isolated from Eu-Myc;CD19-Cre;Odc fl/fl mice and two B cell lymphomas isolated from Eu-Myc;CD19-Cre;Odc +/+. CD19-Cre expression leads to the deletion of Odc specifically in B cells.","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 homeostasis of Eu-Myc Lymphomas","STUDY_TYPE":"Lymphomas isolated from Eu-Myc;CD19-Cre;Odc fl/fl mice","STUDY_SUMMARY":"Amino acid levels analysis of lymphomas isolated from Eu-Myc;CD19-Cre;Odc fl/fl mic and their wild-type counterparts Eu-Myc;CD19-Cre;Odc +/+","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":"Lymphomas isolated from Eu-Myc;CD19-Cre;Odc fl/fl mice in triplicate"},

"SUBJECT":{"SUBJECT_TYPE":"Cells","SUBJECT_SPECIES":"Mus musculus","TAXONOMY_ID":"10090","CELL_STRAIN_DETAILS":"BIT","SUBJECT_COMMENTS":"See study design section for cell number per sample","CELL_PRIMARY_IMMORTALIZED":"Immortalized"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"BIT636",
"Sample ID":"BIT_001",
"Factors":{"Genotype":"Odc +/+"}
},
{
"Subject ID":"BIT636",
"Sample ID":"BIT_002",
"Factors":{"Genotype":"Odc +/+"}
},
{
"Subject ID":"BIT636",
"Sample ID":"BIT_003",
"Factors":{"Genotype":"Odc +/+"}
},
{
"Subject ID":"BIT642",
"Sample ID":"BIT_004",
"Factors":{"Genotype":"Odc +/+"}
},
{
"Subject ID":"BIT642",
"Sample ID":"BIT_005",
"Factors":{"Genotype":"Odc +/+"}
},
{
"Subject ID":"BIT642",
"Sample ID":"BIT_006",
"Factors":{"Genotype":"Odc +/+"}
},
{
"Subject ID":"BIT654",
"Sample ID":"BIT_007",
"Factors":{"Genotype":"Odc -/-"}
},
{
"Subject ID":"BIT654",
"Sample ID":"BIT_008",
"Factors":{"Genotype":"Odc -/-"}
},
{
"Subject ID":"BIT654",
"Sample ID":"BIT_009",
"Factors":{"Genotype":"Odc -/-"}
},
{
"Subject ID":"BIT640",
"Sample ID":"BIT_010",
"Factors":{"Genotype":"Odc -/-"}
},
{
"Subject ID":"BIT640",
"Sample ID":"BIT_011",
"Factors":{"Genotype":"Odc -/-"}
},
{
"Subject ID":"BIT640",
"Sample ID":"BIT_012",
"Factors":{"Genotype":"Odc -/-"}
}
],
"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_TIME":"Collected during log phase","STORAGE_CONDITIONS":"Pellet at -80C","STORAGE_VIALS":"1.5 mL microfuge tube","TISSUE_CELL_IDENTIFICATION":"BIT"},

"TREATMENT":{"TREATMENT_SUMMARY":"Cells were not treated. Cells were collected during log phase","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","BIT_001":"0.92","BIT_002":"0.80","BIT_003":"2.45","BIT_004":"0.88","BIT_005":"1.01","BIT_006":"1.01","BIT_007":"1.47","BIT_008":"1.27","BIT_009":"1.53","BIT_010":"6.52","BIT_011":"5.78","BIT_012":"5.64"},{"Metabolite":"Arginine","BIT_001":"0.07","BIT_002":"0.05","BIT_003":"0.07","BIT_004":"0.05","BIT_005":"0.04","BIT_006":"0.06","BIT_007":"0.06","BIT_008":"0.05","BIT_009":"0.05","BIT_010":"0.11","BIT_011":"0.10","BIT_012":"0.12"},{"Metabolite":"Asparagine","BIT_001":"0.06","BIT_002":"","BIT_003":"0.07","BIT_004":"0.06","BIT_005":"0.05","BIT_006":"0.05","BIT_007":"0.11","BIT_008":"0.09","BIT_009":"0.12","BIT_010":"0.15","BIT_011":"0.14","BIT_012":"0.15"},{"Metabolite":"Aspartate","BIT_001":"0.11","BIT_002":"0.11","BIT_003":"0.09","BIT_004":"0.13","BIT_005":"0.11","BIT_006":"0.10","BIT_007":"0.11","BIT_008":"0.09","BIT_009":"0.16","BIT_010":"1.07","BIT_011":"0.89","BIT_012":"1.26"},{"Metabolite":"Glutamate","BIT_001":"3.80","BIT_002":"3.26","BIT_003":"4.65","BIT_004":"3.72","BIT_005":"3.04","BIT_006":"2.63","BIT_007":"7.46","BIT_008":"5.85","BIT_009":"9.16","BIT_010":"3.58","BIT_011":"3.92","BIT_012":"5.91"},{"Metabolite":"Glutamine","BIT_001":"1.11","BIT_002":"1.12","BIT_003":"1.13","BIT_004":"1.64","BIT_005":"1.49","BIT_006":"1.85","BIT_007":"0.64","BIT_008":"0.43","BIT_009":"0.90","BIT_010":"2.63","BIT_011":"2.32","BIT_012":"2.57"},{"Metabolite":"Glycine","BIT_001":"0.88","BIT_002":"1.01","BIT_003":"1.22","BIT_004":"1.30","BIT_005":"1.30","BIT_006":"1.37","BIT_007":"3.59","BIT_008":"3.31","BIT_009":"2.76","BIT_010":"1.33","BIT_011":"1.58","BIT_012":"1.53"},{"Metabolite":"Histidine","BIT_001":"0.07","BIT_002":"0.05","BIT_003":"0.07","BIT_004":"","BIT_005":"0.05","BIT_006":"0.05","BIT_007":"0.08","BIT_008":"0.06","BIT_009":"0.08","BIT_010":"0.11","BIT_011":"0.11","BIT_012":"0.12"},{"Metabolite":"Isoleucine","BIT_001":"0.13","BIT_002":"0.13","BIT_003":"0.21","BIT_004":"0.11","BIT_005":"0.11","BIT_006":"0.12","BIT_007":"0.14","BIT_008":"0.14","BIT_009":"0.15","BIT_010":"0.20","BIT_011":"0.23","BIT_012":"0.27"},{"Metabolite":"Leucine","BIT_001":"0.12","BIT_002":"0.15","BIT_003":"0.19","BIT_004":"0.08","BIT_005":"0.11","BIT_006":"0.12","BIT_007":"0.14","BIT_008":"0.15","BIT_009":"0.15","BIT_010":"0.26","BIT_011":"0.19","BIT_012":"0.26"},{"Metabolite":"Phenylalanine","BIT_001":"0.09","BIT_002":"0.10","BIT_003":"0.19","BIT_004":"0.07","BIT_005":"0.07","BIT_006":"0.07","BIT_007":"0.12","BIT_008":"0.10","BIT_009":"0.14","BIT_010":"0.17","BIT_011":"0.18","BIT_012":"0.21"},{"Metabolite":"Proline","BIT_001":"0.66","BIT_002":"0.61","BIT_003":"1.29","BIT_004":"0.58","BIT_005":"0.57","BIT_006":"0.65","BIT_007":"1.23","BIT_008":"1.02","BIT_009":"1.10","BIT_010":"0.87","BIT_011":"1.05","BIT_012":"0.90"},{"Metabolite":"Serine","BIT_001":"0.09","BIT_002":"0.08","BIT_003":"","BIT_004":"0.05","BIT_005":"0.05","BIT_006":"","BIT_007":"0.10","BIT_008":"0.09","BIT_009":"0.14","BIT_010":"0.40","BIT_011":"0.34","BIT_012":"0.33"},{"Metabolite":"Threonine","BIT_001":"0.46","BIT_002":"0.30","BIT_003":"0.85","BIT_004":"0.51","BIT_005":"0.63","BIT_006":"0.54","BIT_007":"0.51","BIT_008":"0.53","BIT_009":"0.62","BIT_010":"1.37","BIT_011":"1.24","BIT_012":"1.16"},{"Metabolite":"Tryptophan","BIT_001":"0.02","BIT_002":"0.02","BIT_003":"0.03","BIT_004":"0.02","BIT_005":"0.01","BIT_006":"0.02","BIT_007":"0.03","BIT_008":"0.02","BIT_009":"0.03","BIT_010":"0.04","BIT_011":"0.03","BIT_012":"0.04"},{"Metabolite":"Tyrosine","BIT_001":"0.10","BIT_002":"0.08","BIT_003":"0.16","BIT_004":"0.08","BIT_005":"0.09","BIT_006":"0.09","BIT_007":"0.17","BIT_008":"0.11","BIT_009":"0.13","BIT_010":"0.20","BIT_011":"0.20","BIT_012":"0.19"},{"Metabolite":"Valine","BIT_001":"0.17","BIT_002":"0.14","BIT_003":"0.25","BIT_004":"0.13","BIT_005":"0.12","BIT_006":"0.12","BIT_007":"0.21","BIT_008":"0.15","BIT_009":"0.20","BIT_010":"0.26","BIT_011":"0.27","BIT_012":"0.31"}],

"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":"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":""}]
}

}