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.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
Study ID | ST000341 |
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 |
Hyung-Ok.Lee@fccc.edu | |
Phone | 215-728-3601 |
Submit Date | 2016-01-28 |
Num Groups | 4 |
Total Subjects | 24 |
Raw Data File Type(s) | raw(Thermo) |
Analysis Type Detail | LC-MS |
Release Date | 2017-01-28 |
Release Version | 1 |
Select appropriate tab below to view additional metadata details:
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: | Mammals |
Factors:
Subject type: Animal; Subject species: Mus musculus (Factor headings shown in green)
mb_sample_id | local_sample_id | Tissue | Treatment |
---|---|---|---|
SA015171 | DNA-15 | Bone Marrow | Zn+ |
SA015172 | DNA-16 | Bone Marrow | Zn+ |
SA015173 | DNA-18 | Bone Marrow | Zn+ |
SA015174 | DNA-14 | Bone Marrow | Zn+ |
SA015175 | DNA-17 | Bone Marrow | Zn+ |
SA015176 | DNA-13 | Bone Marrow | Zn+ |
SA015177 | DNA-20 | Bone Marrow | Zn- |
SA015178 | DNA-19 | Bone Marrow | Zn- |
SA015179 | DNA-21 | Bone Marrow | Zn- |
SA015180 | DNA-22 | Bone Marrow | Zn- |
SA015181 | DNA-23 | Bone Marrow | Zn- |
SA015182 | DNA-24 | Bone Marrow | Zn- |
SA015183 | DNA-03 | Liver | Zn+ |
SA015184 | DNA-02 | Liver | Zn+ |
SA015185 | DNA-04 | Liver | Zn+ |
SA015186 | DNA-05 | Liver | Zn+ |
SA015187 | DNA-06 | Liver | Zn+ |
SA015188 | DNA-01 | Liver | Zn+ |
SA015189 | DNA-10 | Liver | Zn- |
SA015190 | DNA-09 | Liver | Zn- |
SA015191 | DNA-11 | Liver | Zn- |
SA015192 | DNA-12 | Liver | Zn- |
SA015193 | DNA-08 | Liver | Zn- |
SA015194 | DNA-07 | Liver | 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 |