Summary of Study ST001635
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 PR001044. The data can be accessed directly via it's Project DOI: 10.21228/M8RD7H 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.
| Study ID | ST001635 |
| Study Title | Higher Dietary Carbohydrates Detrimentally Impact Obesity-Associated Breast Cancer Chemoresistance |
| Study Type | Untargeted UPLC-MS Metabolomics Analysis |
| Study Summary | This study is a part of an ongoing project entitled, “Higher Dietary Carbohydrates Detrimentally Impact Obesity-Associated Breast Cancer Chemoresistance.” (See project). Untargeted LCMS metabolomics analysis was performed to identify metabolic markers of nutritionally dependent and obesity-associated chemoresistance in female C57LB/6 mice fed either a high carbohydrate plus high fat (HCHF) diet or a high protein diet (HP). Mice were fed 15 weeks on either diet, then injected with a MMTV-Wnt-1 mouse mammary basal-like breast cancer cell line, for tumor formation up to 6 weeks. Three mice on either diet were treated for 24 hr with Doxorubicin or Saline as a vehicle control. All samples were analyzed in the positive mode for untargeted metabolomics analysis. Liver samples were selected for analysis because of an observation of fatty liver development in mice only on the HCHF diet after 15 weeks. Samples were extracted and analyzed by UPLS-MS analysis using Q-Exactive HFX mass spectrometer. |
| Institute | University of North Carolina at Chapel Hill |
| Department | Nutrition |
| Laboratory | Metabolomics and Exposome Laboratory, Nutrition Research Institute, UNC Chapel Hill |
| Last Name | Sumner |
| First Name | Susan |
| Address | 500 Laureate Way, Nutrition Research Institute, UNC Chapel Hill |
| susan_sumner@unc.edu | |
| Phone | (919) 622-4456 |
| Submit Date | 2020-12-18 |
| Num Groups | 6 |
| Total Subjects | 193 |
| Num Females | 175 |
| Study Comments | The number of groups includes the QC samples |
| Raw Data Available | Yes |
| Raw Data File Type(s) | raw(Thermo) |
| Analysis Type Detail | LC-MS |
| Release Date | 2021-12-18 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Sample Preparation:
| Sampleprep ID: | SP001718 |
| Sampleprep Summary: | Liver tissue samples were put into randomized order (n=60), then were weighed then sectioned into three lobes (on dry ice) prior to analyses. Tissues were sectioned into the Right lobe, Left lobe and Median lobe (comprised of the caudate+quadrate lobes). Individual lobe weights were measured, then each lobe was further sectioned into equal numbers of cubes (4-6 cubes/lobe), depending on the lobe size. Two-three smaller cubes, were recombined into a new tube, weighed and used for metabolomics analysis. Two mice (HP diet, 5.5 weeks of tumor growth) were missing both left and median lobes from their gross liver tissues, and one mouse (HCHF diet, 5.5 weeks of tumor growth) was missing the median lobe; thus these samples were not included for metabolomics analysis. Thus, the total number of experimental samples was 175 rather than 180. |
| Processing Method: | Sectioned and weighed frozen liver tissue samples (n=175, 60-450 mg) were homogenized with cold methanol (10 µl for every mg of tissue) in a Bead Ruptor Elite Bead Mill Homogenizer (OMNI International) at 5.0 m/s for 30 s in two cycles. The supernatants were collected after centrifugation at 16,000 rcf for 20 min at 4 °C. A quality control pool (QC pool) sample was prepared by pooling 30 µL supernatant aliquots from selected individual samples (n=78), with a total pre-processing weight ≥ 60 mg. The supernatants (200 µL) of each study sample and QC pools were transferred to new tubes and dried under Speed-vac. Each dried sample was reconstituted in a 200 µL water-methanol (95:5) solution containing 500 ng/ml L-tryphotophan-d5. The samples were thoroughly mixed on multiple tube vortexer for 10 mins at 5000 rpm. Samples were centrifuged at room temperature and at 16,000 rcf for 4 min. The supernatant was transferred to pre-labeled auto-sampler vials for data acquisition. Untargeted metabolomics was conducted using a Thermo Scientific™ Vanquish™ UPHPLC - Q Exactive™ HF-X Orbitrap System. Metabolites were separated on an Acquity UPLC HSS T3 C18 (2.1 X 100 mm, 1.8 µm) operating at 50 °C using a reversed phase gradient separation with Water with 0.1% Formic Acid (v/v) as mobile phase A and Methanol with 0.1% Formic Acid (v/v) as mobile phase B. A 5 µL amount was injected into the instrument, and MS data was collected between 50-750 m/z in the positive mode with the MS/MS data triggered by the Data-Dependent Acquisition. |
| Processing Storage Conditions: | 4℃ |
| Extract Storage: | -80℃ |
