#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         	┬Ámol/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