{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST000341","ANALYSIS_ID":"AN000553","VERSION":"1","CREATED_ON":"January 28, 2016, 4:00 pm"},

"PROJECT":{"PROJECT_TITLE":"Methylation in mouse liver","PROJECT_TYPE":"DNA Methylation","PROJECT_SUMMARY":"We are interested in knowing whether elevated total homocysteine affects the level of DNA methylation liver cells and Bone Marrow in our inducible mouse model of hyperhomocysteinemia. To answer this question, we will use our Tg-hCBS Cbs-/- mouse. This mouse lacks the endogenous mouse CBS gene and instead contains a human CBS cDNA transgene that is under control of a zinc inducible MT-1 promoter. We will send you DNA isolated from the livers and Bone Marrow of twelve animals, six of which that were uninduced and six that were induced by treatment with zinc water.","INSTITUTE":"Fox Chase Cancer Center","DEPARTMENT":"Cancer Biology","LABORATORY":"Kruger","LAST_NAME":"Kruger","FIRST_NAME":"Warren","ADDRESS":"Fox Chase Cancer Center, 333 Cottman Ave., Philadelphia, PA 19111","EMAIL":"warren.kruger@fccc.edu","PHONE":"215-728-3030","FUNDING_SOURCE":"R01GM098772-04"},

"STUDY":{"STUDY_TITLE":"Methylation in mouse lymphomas","STUDY_TYPE":"Case-Control (3 groups)","STUDY_SUMMARY":"We want to determine if there is a difference in the DNA methylation status of liver and Bone marrow in Cbs-/- mice under + or - ZnH20.","INSTITUTE":"University of Florida","DEPARTMENT":"SECIM","LABORATORY":"Kruger - Cancer Biology","LAST_NAME":"Lee","FIRST_NAME":"Hyung-Ok","ADDRESS":"Fox Chase Cancer Center, 333 Cottman Ave., Philadelphia, PA 19111","EMAIL":"Hyung-Ok.Lee@fccc.edu","PHONE":"215-728-3601","NUM_GROUPS":"4","TOTAL_SUBJECTS":"24"},

"SUBJECT":{"SUBJECT_TYPE":"Animal","SUBJECT_SPECIES":"Mus musculus","TAXONOMY_ID":"10090","GENOTYPE_STRAIN":"C57BL6","AGE_OR_AGE_RANGE":"15 weeks","WEIGHT_OR_WEIGHT_RANGE":"20-30g","GENDER":"Female","ANIMAL_WATER":"with or without Zn"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"-",
"Sample ID":"DNA-01",
"Factors":{"Tissue":"Liver","Treatment":"Zn+"},
"Additional sample data":{"Gender":"F","Genotype":"Tg-cbs-/-","Mouse #":"810"}
},
{
"Subject ID":"-",
"Sample ID":"DNA-02",
"Factors":{"Tissue":"Liver","Treatment":"Zn+"},
"Additional sample data":{"Gender":"F","Genotype":"Tg-cbs-/-","Mouse #":"824"}
},
{
"Subject ID":"-",
"Sample ID":"DNA-03",
"Factors":{"Tissue":"Liver","Treatment":"Zn+"},
"Additional sample data":{"Gender":"F","Genotype":"Tg-cbs-/-","Mouse #":"834"}
},
{
"Subject ID":"-",
"Sample ID":"DNA-04",
"Factors":{"Tissue":"Liver","Treatment":"Zn+"},
"Additional sample data":{"Gender":"F","Genotype":"Tg-cbs-/-","Mouse #":"840"}
},
{
"Subject ID":"-",
"Sample ID":"DNA-05",
"Factors":{"Tissue":"Liver","Treatment":"Zn+"},
"Additional sample data":{"Gender":"F","Genotype":"Tg-cbs-/-","Mouse #":"841"}
},
{
"Subject ID":"-",
"Sample ID":"DNA-06",
"Factors":{"Tissue":"Liver","Treatment":"Zn+"},
"Additional sample data":{"Gender":"F","Genotype":"Tg-cbs-/-","Mouse #":"866"}
},
{
"Subject ID":"-",
"Sample ID":"DNA-07",
"Factors":{"Tissue":"Liver","Treatment":"Zn-"},
"Additional sample data":{"Gender":"F","Genotype":"Tg-cbs-/-","Mouse #":"811"}
},
{
"Subject ID":"-",
"Sample ID":"DNA-08",
"Factors":{"Tissue":"Liver","Treatment":"Zn-"},
"Additional sample data":{"Gender":"F","Genotype":"Tg-cbs-/-","Mouse #":"830"}
},
{
"Subject ID":"-",
"Sample ID":"DNA-09",
"Factors":{"Tissue":"Liver","Treatment":"Zn-"},
"Additional sample data":{"Gender":"F","Genotype":"Tg-cbs-/-","Mouse #":"833"}
},
{
"Subject ID":"-",
"Sample ID":"DNA-10",
"Factors":{"Tissue":"Liver","Treatment":"Zn-"},
"Additional sample data":{"Gender":"F","Genotype":"Tg-cbs-/-","Mouse #":"842"}
},
{
"Subject ID":"-",
"Sample ID":"DNA-11",
"Factors":{"Tissue":"Liver","Treatment":"Zn-"},
"Additional sample data":{"Gender":"F","Genotype":"Tg-cbs-/-","Mouse #":"843"}
},
{
"Subject ID":"-",
"Sample ID":"DNA-12",
"Factors":{"Tissue":"Liver","Treatment":"Zn-"},
"Additional sample data":{"Gender":"F","Genotype":"Tg-cbs-/-","Mouse #":"871"}
},
{
"Subject ID":"-",
"Sample ID":"DNA-13",
"Factors":{"Tissue":"Bone Marrow","Treatment":"Zn+"},
"Additional sample data":{"Gender":"F","Genotype":"Tg-cbs-/-","Mouse #":"810"}
},
{
"Subject ID":"-",
"Sample ID":"DNA-14",
"Factors":{"Tissue":"Bone Marrow","Treatment":"Zn+"},
"Additional sample data":{"Gender":"F","Genotype":"Tg-cbs-/-","Mouse #":"824"}
},
{
"Subject ID":"-",
"Sample ID":"DNA-15",
"Factors":{"Tissue":"Bone Marrow","Treatment":"Zn+"},
"Additional sample data":{"Gender":"F","Genotype":"Tg-cbs-/-","Mouse #":"834"}
},
{
"Subject ID":"-",
"Sample ID":"DNA-16",
"Factors":{"Tissue":"Bone Marrow","Treatment":"Zn+"},
"Additional sample data":{"Gender":"F","Genotype":"Tg-cbs-/-","Mouse #":"840"}
},
{
"Subject ID":"-",
"Sample ID":"DNA-17",
"Factors":{"Tissue":"Bone Marrow","Treatment":"Zn+"},
"Additional sample data":{"Gender":"F","Genotype":"Tg-cbs-/-","Mouse #":"841"}
},
{
"Subject ID":"-",
"Sample ID":"DNA-18",
"Factors":{"Tissue":"Bone Marrow","Treatment":"Zn+"},
"Additional sample data":{"Gender":"F","Genotype":"Tg-cbs-/-","Mouse #":"866"}
},
{
"Subject ID":"-",
"Sample ID":"DNA-19",
"Factors":{"Tissue":"Bone Marrow","Treatment":"Zn-"},
"Additional sample data":{"Gender":"F","Genotype":"Tg-cbs-/-","Mouse #":"811"}
},
{
"Subject ID":"-",
"Sample ID":"DNA-20",
"Factors":{"Tissue":"Bone Marrow","Treatment":"Zn-"},
"Additional sample data":{"Gender":"F","Genotype":"Tg-cbs-/-","Mouse #":"830"}
},
{
"Subject ID":"-",
"Sample ID":"DNA-21",
"Factors":{"Tissue":"Bone Marrow","Treatment":"Zn-"},
"Additional sample data":{"Gender":"F","Genotype":"Tg-cbs-/-","Mouse #":"833"}
},
{
"Subject ID":"-",
"Sample ID":"DNA-22",
"Factors":{"Tissue":"Bone Marrow","Treatment":"Zn-"},
"Additional sample data":{"Gender":"F","Genotype":"Tg-cbs-/-","Mouse #":"842"}
},
{
"Subject ID":"-",
"Sample ID":"DNA-23",
"Factors":{"Tissue":"Bone Marrow","Treatment":"Zn-"},
"Additional sample data":{"Gender":"F","Genotype":"Tg-cbs-/-","Mouse #":"843"}
},
{
"Subject ID":"-",
"Sample ID":"DNA-24",
"Factors":{"Tissue":"Bone Marrow","Treatment":"Zn-"},
"Additional sample data":{"Gender":"F","Genotype":"Tg-cbs-/-","Mouse #":"871"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"DNA will be provided in TE solution. Concentrations are on Metadata sheet.","COLLECTION_PROTOCOL_FILENAME":"MeDNA_SOP.pdf","SAMPLE_TYPE":"Liver DNA in 10mM Tris-HCl, 1 mM EDTA(pH 7.5) & Bone Marrow DNA in 10mM Tris-HCl, 0.5mM EDTA (pH 9.0)","COLLECTION_METHOD":"Dissection followed by DNA prep","COLLECTION_LOCATION":"Our Lab","COLLECTION_FREQUENCY":"once","COLLECTION_DURATION":"A few minutes.","VOLUMEORAMOUNT_COLLECTED":"19-20 ul","STORAGE_CONDITIONS":"-20C","STORAGE_VIALS":"eppendorf tubes"},

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

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"See file attached.","SAMPLEPREP_PROTOCOL_FILENAME":"MeDNA_SOP.pdf"},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_SUMMARY":"See file","CHROMATOGRAPHY_TYPE":"Reversed phase","INSTRUMENT_NAME":"Thermo Accela","COLUMN_NAME":"Phenomenex Luna C18 (150 x 2mm)","FLOW_RATE":"300 uL/min.","METHODS_FILENAME":"MeDNA_SOP.pdf"},

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

"MS":{"MS_COMMENTS":"-","INSTRUMENT_NAME":"Thermo Quantum Ultra","INSTRUMENT_TYPE":"Triple quadrupole","MS_TYPE":"ESI","ION_MODE":"POSITIVE"},

"MS_METABOLITE_DATA":{
"Units":"┬Ámol/l",

"Data":[{"Metabolite":"2'-deoxycytidine","DNA-01":"4.258442","DNA-02":"3.443514","DNA-03":"6.093914","DNA-04":"2.018201","DNA-05":"3.172706","DNA-06":"2.804562","DNA-07":"6.543767","DNA-08":"2.479491","DNA-09":"2.906419","DNA-10":"1.947787","DNA-11":"2.620428","DNA-12":"2.644327","DNA-13":"3.434737","DNA-14":"5.678731","DNA-15":"3.110693","DNA-16":"5.815776","DNA-17":"6.565538","DNA-18":"4.452710","DNA-19":"7.384910","DNA-20":"4.322390","DNA-21":"7.665130","DNA-22":"7.790976","DNA-23":"7.659455","DNA-24":"4.562573"},{"Metabolite":"5-Methyl-2'-deoxycytidine","DNA-01":"0.175359","DNA-02":"0.140281","DNA-03":"0.236333","DNA-04":"0.075033","DNA-05":"0.123768","DNA-06":"0.110288","DNA-07":"0.265071","DNA-08":"0.097237","DNA-09":"0.113913","DNA-10":"0.071348","DNA-11":"0.102249","DNA-12":"0.094565","DNA-13":"0.120294","DNA-14":"0.210159","DNA-15":"0.109573","DNA-16":"0.201070","DNA-17":"0.232489","DNA-18":"0.156612","DNA-19":"0.264654","DNA-20":"0.145707","DNA-21":"0.279287","DNA-22":"0.276848","DNA-23":"0.271707","DNA-24":"0.160264"}],

"Metabolites":[{"Metabolite":"2'-deoxycytidine","retention index":"1.7","quantified m/z":"112.1","PubChem ID":"13711","KEGG ID":""},{"Metabolite":"5-Methyl-2'-deoxycytidine","retention index":"2.8","quantified m/z":"126.1","PubChem ID":"13279","KEGG ID":""}]
}

}