Summary of Study ST000341

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR000273. The data can be accessed directly via it's Project DOI: 10.21228/M8H30K This work is supported by NIH grant, U2C- DK119886.

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Study IDST000341
Study TitleMethylation in mouse lymphomas
Study TypeCase-Control (3 groups)
Study SummaryWe 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
DepartmentSECIM
LaboratoryKruger - Cancer Biology
Last NameLee
First NameHyung-Ok
AddressFox Chase Cancer Center, 333 Cottman Ave., Philadelphia, PA 19111
EmailHyung-Ok.Lee@fccc.edu
Phone215-728-3601
Submit Date2016-01-28
Num Groups4
Total Subjects24
Raw Data File Type(s)raw(Thermo)
Analysis Type DetailLC-MS
Release Date2017-01-28
Release Version1
Hyung-Ok Lee Hyung-Ok Lee
https://dx.doi.org/10.21228/M8H30K
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR000273
Project DOI:doi: 10.21228/M8H30K
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

Subject:

Subject ID:SU000361
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
Species Group:Mammal

Factors:

Subject type: Animal; Subject species: Mus musculus (Factor headings shown in green)

mb_sample_id local_sample_id Tissue Treatment
SA015171DNA-15Bone Marrow Zn+
SA015172DNA-16Bone Marrow Zn+
SA015173DNA-18Bone Marrow Zn+
SA015174DNA-14Bone Marrow Zn+
SA015175DNA-17Bone Marrow Zn+
SA015176DNA-13Bone Marrow Zn+
SA015177DNA-20Bone Marrow Zn-
SA015178DNA-19Bone Marrow Zn-
SA015179DNA-21Bone Marrow Zn-
SA015180DNA-22Bone Marrow Zn-
SA015181DNA-23Bone Marrow Zn-
SA015182DNA-24Bone Marrow Zn-
SA015183DNA-03Liver Zn+
SA015184DNA-02Liver Zn+
SA015185DNA-04Liver Zn+
SA015186DNA-05Liver Zn+
SA015187DNA-06Liver Zn+
SA015188DNA-01Liver Zn+
SA015189DNA-10Liver Zn-
SA015190DNA-09Liver Zn-
SA015191DNA-11Liver Zn-
SA015192DNA-12Liver Zn-
SA015193DNA-08Liver Zn-
SA015194DNA-07Liver Zn-
Showing results 1 to 24 of 24

Collection:

Collection ID:CO000355
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 ID:TR000375
Treatment Summary:None

Sample Preparation:

Sampleprep ID:SP000368
Sampleprep Summary:See file attached.
Sampleprep Protocol Filename:MeDNA_SOP.pdf

Combined analysis:

Analysis ID AN000553
Analysis type MS
Chromatography type Reversed phase
Chromatography system Thermo Accela
Column Phenomenex Luna C18 (150 x 2mm)
MS Type ESI
MS instrument type Triple quadrupole
MS instrument name Thermo Quantum Ultra
Ion Mode POSITIVE
Units µmol/l

Chromatography:

Chromatography ID:CH000390
Chromatography Summary:See file
Methods Filename:MeDNA_SOP.pdf
Instrument Name:Thermo Accela
Column Name:Phenomenex Luna C18 (150 x 2mm)
Flow Rate:300 uL/min.
Chromatography Type:Reversed phase

MS:

MS ID:MS000489
Analysis ID:AN000553
Instrument Name:Thermo Quantum Ultra
Instrument Type:Triple quadrupole
MS Type:ESI
Ion Mode:POSITIVE
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