Summary of study ST000054

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 PR000051. The data can be accessed directly via it's Project DOI: 10.21228/M8MS3J This work is supported by NIH grant, U2C- DK119886.

See: https://www.metabolomicsworkbench.org/about/howtocite.php

This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.

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Study IDST000054
Study TitleMetabolic Microenvironments in Normal Breast and Breast Cancer (MS analysis)
Study TypeMetabolomic analysis of normal breast tissue
Study SummaryThe purpose of this study was to understand the metabolomic changes in a breast tissue microenvironment at various stages of cancer development and progression (i.e. normal breast, DCIS, and invasive cancer). The goal of this metabolomics pilot and feasibility study was to apply a broad spectrum GC-MS metabolomics method to determine whether changes in normal tissue of women with cancer correlate with progression and or the subtype of the disease.
Institute
University of North Carolina
DepartmentSystems and Translational Sciences
LaboratorySumner Lab
Last NameSumner
First NameSusan
AddressEastern Regional Comprehensive Metabolomics Resource Core, UNC Nutrition Research Institute, 500 Laureate Way, Kannapolis, NC, 28081
Emailsusan_sumner @unc.edu
Phone704-250-5066
Submit Date2014-04-30
Num Groups8
Total Subjects192
Study Commentssample preparation and analysis randomized with data collection over multiple days
Publications1. Brauer HA, Makowski L, Hoadley KA, Casbas-Hernandez P, Lang LJ, Roman-Perez E, D’Arcy M, Freemerman AJ, Perou CM, Troester MA: Impact of tumor microenvironment and epithelial phenotypes on metabolism in breast cancer. Clin Cancer Res 2012;19:571-585. 2. J Budczies, C Denkert, B Muller, S Brockmoller, F Klauschen, B Gyorffy, M Dietel, C Richter-Ehrenstein, U Marten, R Salek, J Griffin, M Hilvo, M Oresic, G Wohlgemuth, O Fiehn: Remodeling of central metabolism in invasive breast cancer compared to normal breast tissue – a GC-TOFMS based metabolomics study. BMC Genomics 2012; 13:334.
Raw Data AvailableYes
Raw Data File Type(s).cdf files
Uploaded File Size8.4 G
Analysis Type DetailGC-MS
Release Date2018-08-27
Release Version1
Susan Sumner Susan Sumner
https://dx.doi.org/10.21228/M8MS3J
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Sample Preparation:

Sampleprep ID:SP000069
Sampleprep Summary:Breast tissue samples were homogenized in 3:3:2 (acetonitrile:isopropanol:water) at a concentration of 100 mg/mL. Samples dried and extracted into 50% acetonitrile. Sample dried and aliquot taken for NMR. Sample returned and extract processed for GC/MS analysis. Samples were derivatized using 2 step derivatization method (methoximation with methoxy amine followed by TMS derivatization with MSTFA).
Sampleprep Protocol Filename:RTI_MT_Breast_Tissue_Procedures_GC-TOF-MS.docx
Processing Method:Homogenization and Solvent Removal with SpeedVac
Processing Storage Conditions:4°C
Extraction Method:3:3:2 (acetonitrile:isopropanol:water) and then 50% Acetonitrile
Extract Concentration Dilution:dried on SpeedVac
Extract Storage:-80°C
Sample Resuspension:resuspended in D2O + Chenomix ISTD solution
Sample Derivatization:Methoximation with methoxy amine at 40 mg/ml in pyridine followed by TMS derivatization with MSTFA
Sample Spiking:FAMES (C8-C30) added to MSTFA as retention time markers
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