#METABOLOMICS WORKBENCH kenanazam_20160128_120627 STUDY_ID:ST000341 ANALYSIS_ID:AN000553 PROJECT_ID:PR000273 VERSION 1 CREATED_ON January 28, 2016, 4:00 pm #PROJECT PR:PROJECT_TITLE Methylation in mouse liver PR:PROJECT_TYPE DNA Methylation PR:PROJECT_SUMMARY We are interested in knowing whether elevated total homocysteine affects the PR:PROJECT_SUMMARY level of DNA methylation liver cells and Bone Marrow in our inducible mouse PR:PROJECT_SUMMARY model of hyperhomocysteinemia. To answer this question, we will use our Tg-hCBS PR:PROJECT_SUMMARY Cbs-/- mouse. This mouse lacks the endogenous mouse CBS gene and instead PR:PROJECT_SUMMARY contains a human CBS cDNA transgene that is under control of a zinc inducible PR:PROJECT_SUMMARY MT-1 promoter. We will send you DNA isolated from the livers and Bone Marrow of PR:PROJECT_SUMMARY twelve animals, six of which that were uninduced and six that were induced by PR:PROJECT_SUMMARY treatment with zinc water. PR:INSTITUTE Fox Chase Cancer Center PR:DEPARTMENT Cancer Biology PR:LABORATORY Kruger PR:LAST_NAME Kruger PR:FIRST_NAME Warren PR:ADDRESS Fox Chase Cancer Center, 333 Cottman Ave., Philadelphia, PA 19111 PR:EMAIL warren.kruger@fccc.edu PR:PHONE 215-728-3030 PR:FUNDING_SOURCE R01GM098772-04 #STUDY ST:STUDY_TITLE Methylation in mouse lymphomas ST:STUDY_TYPE Case-Control (3 groups) ST:STUDY_SUMMARY We want to determine if there is a difference in the DNA methylation status of ST:STUDY_SUMMARY liver and Bone marrow in Cbs-/- mice under + or - ZnH20. ST:INSTITUTE University of Florida ST:DEPARTMENT SECIM ST:LABORATORY Kruger - Cancer Biology ST:LAST_NAME Lee ST:FIRST_NAME Hyung-Ok ST:ADDRESS Fox Chase Cancer Center, 333 Cottman Ave., Philadelphia, PA 19111 ST:EMAIL Hyung-Ok.Lee@fccc.edu ST:PHONE 215-728-3601 ST:NUM_GROUPS 4 ST:TOTAL_SUBJECTS 24 #SUBJECT SU:SUBJECT_TYPE Animal SU:SUBJECT_SPECIES Mus musculus SU:TAXONOMY_ID 10090 SU:GENOTYPE_STRAIN C57BL6 SU:AGE_OR_AGE_RANGE 15 weeks SU:WEIGHT_OR_WEIGHT_RANGE 20-30g SU:GENDER Female SU:ANIMAL_WATER with or without Zn #SUBJECT_SAMPLE_FACTORS: SUBJECT(optional)[tab]SAMPLE[tab]FACTORS(NAME:VALUE pairs separated by |)[tab]Additional sample data SUBJECT_SAMPLE_FACTORS - DNA-01 Tissue:Liver | Treatment:Zn+ Gender=F; Genotype=Tg-cbs-/-; Mouse #=810 SUBJECT_SAMPLE_FACTORS - DNA-02 Tissue:Liver | Treatment:Zn+ Gender=F; Genotype=Tg-cbs-/-; Mouse #=824 SUBJECT_SAMPLE_FACTORS - DNA-03 Tissue:Liver | Treatment:Zn+ Gender=F; Genotype=Tg-cbs-/-; Mouse #=834 SUBJECT_SAMPLE_FACTORS - DNA-04 Tissue:Liver | Treatment:Zn+ Gender=F; Genotype=Tg-cbs-/-; Mouse #=840 SUBJECT_SAMPLE_FACTORS - DNA-05 Tissue:Liver | Treatment:Zn+ Gender=F; Genotype=Tg-cbs-/-; Mouse #=841 SUBJECT_SAMPLE_FACTORS - DNA-06 Tissue:Liver | Treatment:Zn+ Gender=F; Genotype=Tg-cbs-/-; Mouse #=866 SUBJECT_SAMPLE_FACTORS - DNA-07 Tissue:Liver | Treatment:Zn- Gender=F; Genotype=Tg-cbs-/-; Mouse #=811 SUBJECT_SAMPLE_FACTORS - DNA-08 Tissue:Liver | Treatment:Zn- Gender=F; Genotype=Tg-cbs-/-; Mouse #=830 SUBJECT_SAMPLE_FACTORS - DNA-09 Tissue:Liver | Treatment:Zn- Gender=F; Genotype=Tg-cbs-/-; Mouse #=833 SUBJECT_SAMPLE_FACTORS - DNA-10 Tissue:Liver | Treatment:Zn- Gender=F; Genotype=Tg-cbs-/-; Mouse #=842 SUBJECT_SAMPLE_FACTORS - DNA-11 Tissue:Liver | Treatment:Zn- Gender=F; Genotype=Tg-cbs-/-; Mouse #=843 SUBJECT_SAMPLE_FACTORS - DNA-12 Tissue:Liver | Treatment:Zn- Gender=F; Genotype=Tg-cbs-/-; Mouse #=871 SUBJECT_SAMPLE_FACTORS - DNA-13 Tissue:Bone Marrow | Treatment:Zn+ Gender=F; Genotype=Tg-cbs-/-; Mouse #=810 SUBJECT_SAMPLE_FACTORS - DNA-14 Tissue:Bone Marrow | Treatment:Zn+ Gender=F; Genotype=Tg-cbs-/-; Mouse #=824 SUBJECT_SAMPLE_FACTORS - DNA-15 Tissue:Bone Marrow | Treatment:Zn+ Gender=F; Genotype=Tg-cbs-/-; Mouse #=834 SUBJECT_SAMPLE_FACTORS - DNA-16 Tissue:Bone Marrow | Treatment:Zn+ Gender=F; Genotype=Tg-cbs-/-; Mouse #=840 SUBJECT_SAMPLE_FACTORS - DNA-17 Tissue:Bone Marrow | Treatment:Zn+ Gender=F; Genotype=Tg-cbs-/-; Mouse #=841 SUBJECT_SAMPLE_FACTORS - DNA-18 Tissue:Bone Marrow | Treatment:Zn+ Gender=F; Genotype=Tg-cbs-/-; Mouse #=866 SUBJECT_SAMPLE_FACTORS - DNA-19 Tissue:Bone Marrow | Treatment:Zn- Gender=F; Genotype=Tg-cbs-/-; Mouse #=811 SUBJECT_SAMPLE_FACTORS - DNA-20 Tissue:Bone Marrow | Treatment:Zn- Gender=F; Genotype=Tg-cbs-/-; Mouse #=830 SUBJECT_SAMPLE_FACTORS - DNA-21 Tissue:Bone Marrow | Treatment:Zn- Gender=F; Genotype=Tg-cbs-/-; Mouse #=833 SUBJECT_SAMPLE_FACTORS - DNA-22 Tissue:Bone Marrow | Treatment:Zn- Gender=F; Genotype=Tg-cbs-/-; Mouse #=842 SUBJECT_SAMPLE_FACTORS - DNA-23 Tissue:Bone Marrow | Treatment:Zn- Gender=F; Genotype=Tg-cbs-/-; Mouse #=843 SUBJECT_SAMPLE_FACTORS - DNA-24 Tissue:Bone Marrow | Treatment:Zn- Gender=F; Genotype=Tg-cbs-/-; Mouse #=871 #COLLECTION CO:COLLECTION_SUMMARY DNA will be provided in TE solution. Concentrations are on Metadata sheet. CO:COLLECTION_PROTOCOL_FILENAME MeDNA_SOP.pdf CO:SAMPLE_TYPE Liver DNA in 10mM Tris-HCl, 1 mM EDTA(pH 7.5) & Bone Marrow DNA in 10mM CO:SAMPLE_TYPE Tris-HCl, 0.5mM EDTA (pH 9.0) CO:COLLECTION_METHOD Dissection followed by DNA prep CO:COLLECTION_LOCATION Our Lab CO:COLLECTION_FREQUENCY once CO:COLLECTION_DURATION A few minutes. CO:VOLUMEORAMOUNT_COLLECTED 19-20 ul CO:STORAGE_CONDITIONS -20C CO:STORAGE_VIALS eppendorf tubes #TREATMENT TR:TREATMENT_SUMMARY None #SAMPLEPREP SP:SAMPLEPREP_SUMMARY See file attached. SP:SAMPLEPREP_PROTOCOL_FILENAME MeDNA_SOP.pdf #CHROMATOGRAPHY CH:CHROMATOGRAPHY_SUMMARY See file CH:CHROMATOGRAPHY_TYPE Reversed phase CH:INSTRUMENT_NAME Thermo Accela CH:COLUMN_NAME Phenomenex Luna C18 (150 x 2mm) CH:FLOW_RATE 300 uL/min. CH:METHODS_FILENAME MeDNA_SOP.pdf #ANALYSIS AN:ANALYSIS_TYPE MS #MS MS:MS_COMMENTS - MS:INSTRUMENT_NAME Thermo Quantum Ultra MS:INSTRUMENT_TYPE Triple quadrupole MS:MS_TYPE ESI MS:ION_MODE POSITIVE #MS_METABOLITE_DATA MS_METABOLITE_DATA:UNITS µmol/l MS_METABOLITE_DATA_START Samples DNA-01 DNA-02 DNA-03 DNA-04 DNA-05 DNA-06 DNA-07 DNA-08 DNA-09 DNA-10 DNA-11 DNA-12 DNA-13 DNA-14 DNA-15 DNA-16 DNA-17 DNA-18 DNA-19 DNA-20 DNA-21 DNA-22 DNA-23 DNA-24 Factors Tissue:Liver | Treatment:Zn+ Tissue:Liver | Treatment:Zn+ Tissue:Liver | Treatment:Zn+ Tissue:Liver | Treatment:Zn+ Tissue:Liver | Treatment:Zn+ Tissue:Liver | Treatment:Zn+ Tissue:Liver | Treatment:Zn- Tissue:Liver | Treatment:Zn- Tissue:Liver | Treatment:Zn- Tissue:Liver | Treatment:Zn- Tissue:Liver | Treatment:Zn- Tissue:Liver | Treatment:Zn- Tissue:Bone Marrow | Treatment:Zn+ Tissue:Bone Marrow | Treatment:Zn+ Tissue:Bone Marrow | Treatment:Zn+ Tissue:Bone Marrow | Treatment:Zn+ Tissue:Bone Marrow | Treatment:Zn+ Tissue:Bone Marrow | Treatment:Zn+ Tissue:Bone Marrow | Treatment:Zn- Tissue:Bone Marrow | Treatment:Zn- Tissue:Bone Marrow | Treatment:Zn- Tissue:Bone Marrow | Treatment:Zn- Tissue:Bone Marrow | Treatment:Zn- Tissue:Bone Marrow | Treatment:Zn- 2'-deoxycytidine 4.258442 3.443514 6.093914 2.018201 3.172706 2.804562 6.543767 2.479491 2.906419 1.947787 2.620428 2.644327 3.434737 5.678731 3.110693 5.815776 6.565538 4.452710 7.384910 4.322390 7.665130 7.790976 7.659455 4.562573 5-Methyl-2'-deoxycytidine 0.175359 0.140281 0.236333 0.075033 0.123768 0.110288 0.265071 0.097237 0.113913 0.071348 0.102249 0.094565 0.120294 0.210159 0.109573 0.201070 0.232489 0.156612 0.264654 0.145707 0.279287 0.276848 0.271707 0.160264 MS_METABOLITE_DATA_END #METABOLITES METABOLITES_START metabolite_name retention index quantified m/z PubChem ID KEGG ID 2'-deoxycytidine 1.7 112.1 13711 5-Methyl-2'-deoxycytidine 2.8 126.1 13279 METABOLITES_END #END