Summary of Study ST001687
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 PR001085. The data can be accessed directly via it's Project DOI: 10.21228/M8FT4Q 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 | ST001687 |
| Study Title | Non-transformed cells respond to fat by inducing glucose metabolism |
| Study Summary | C57BL/6N mice were obtained from the KU Leuven animal laboratory. 2-week old mice were injected i.p. diethylnitrosamine (DEN, 25 mg/Kg) in phosphate buffered saline (3.17 mg/ml).s At 6-weeks of age, mice were randomized into two groups: control diet (CD, E15742-33 ssniff Spezialdiäten GmbH) or high fat diet (HFD, S8655-E220 sniff Spezialdiäten GmbH). At endpoint, mice were sacrificed by injecting approximately 50 µl of a 60 mg/ml Nembutal solution (Vetoquinol). Tissues were immediately excised, washed in ice-cold saline, placed into pre-labelled bags and frozen using a liquid nitrogen-cooled biosqueezer. The bags were then placed in liquid nitrogen until all collections were finished and finally stored at -80°C until further processing. Where necessary tumors were rapidly separated from normal tissue prior to freezing with tumor and normal tissue being stored separately. |
| Institute | VIB-KU Leuven Center for Cancer Biology |
| Department | Department of Oncology |
| Laboratory | Laboratory of Cellular Metabolism and Metabolic Regulation |
| Last Name | Fendt |
| First Name | Sarah-Maria |
| Address | ON IV Herestraat 49 - box 912 3000 Leuven |
| sarah-maria.fendt@kuleuven.be | |
| Phone | +32 16 37 32 61 |
| Submit Date | 2021-02-04 |
| Num Groups | 4 |
| Total Subjects | 16 |
| Num Males | 16 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzML |
| Analysis Type Detail | LC-MS |
| Release Date | 2021-02-27 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR001085 |
| Project DOI: | doi: 10.21228/M8FT4Q |
| Project Title: | Non-transformed cells respond to fat by inducing glucose metabolism |
| Project Summary: | In this study, C57BL/6 mice were exposed to control or high fat diet, and PBS control or diethylnitrosamine (DEN) injections for stimulation of hepatocellular carcinoma. This dataset provides untargeted lipidomics in liver tissue from PBS-injected control and high fat diet fed mice, and paired tumor tissue and adjacent liver tissue from DEN-injected, high fat diet fed mice. |
| Institute: | VIB-KU Leuven Center for Cancer Biology |
| Department: | Department of Oncology |
| Laboratory: | Laboratory of Cellular Metabolism and Metabolic Regulation |
| Last Name: | Fendt |
| First Name: | Sarah-Maria |
| Address: | ON IV Herestraat 49 - box 912 3000 Leuven |
| Email: | sarah-maria.fendt@kuleuven.be |
| Phone: | +32 16 37 32 61 |
| Contributors: | Sarah-Maria Fendt, Lindsay A. Broadfield, Jonas Dehairs, Johannes V. Swinnen |
Subject:
| Subject ID: | SU001764 |
| Subject Type: | Mammal |
| Subject Species: | Mus musculus |
| Taxonomy ID: | 10090 |
| Genotype Strain: | C57Bl/6N |
| Age Or Age Range: | 35 weeks |
| Gender: | Male |
| Animal Animal Supplier: | KU Leuven Animal Laboratory |
| Animal Feed: | control diet (E15742-33 ssniff Spezialdiäten GmbH) or 60% high fat diet (S8655-E220 sniff Spezialdiäten GmbH) |
Factors:
Subject type: Mammal; Subject species: Mus musculus (Factor headings shown in green)
| mb_sample_id | local_sample_id | Tissue | Diet | DEN |
|---|---|---|---|---|
| SA155491 | CD-PBS_3.1.2 | Liver | CD | No |
| SA155492 | CD-PBS_3.2.3 | Liver | CD | No |
| SA155493 | CD-PBS_3.2.1 | Liver | CD | No |
| SA155494 | CD-PBS_3.1.4 | Liver | CD | No |
| SA155495 | HFD-PBS_3.5.3 | Liver | HFD | No |
| SA155496 | HFD-PBS_3.4.4 | Liver | HFD | No |
| SA155497 | HFD-PBS_3.4.3 | Liver | HFD | No |
| SA155498 | HFD-PBS_3.5.1 | Liver | HFD | No |
| SA155499 | HFD-DEN_3D20.2L | Liver | HFD | Yes |
| SA155500 | HFD-DEN_3D20.1L | Liver | HFD | Yes |
| SA155501 | HFD-DEN_3D19.1L | Liver | HFD | Yes |
| SA155502 | HFD-DEN_3D19.2L | Liver | HFD | Yes |
| SA155503 | HFD-DEN_3D19.1T | Tumor | HFD | Yes |
| SA155504 | HFD-DEN_3D20.2T | Tumor | HFD | Yes |
| SA155505 | HFD-DEN_3D19.2T | Tumor | HFD | Yes |
| SA155506 | HFD-DEN_3D20.1T | Tumor | HFD | Yes |
| Showing results 1 to 16 of 16 |
Collection:
| Collection ID: | CO001757 |
| Collection Summary: | At endpoint, mice were sacrificed by injecting approximately 50 µl of a 60 mg/ml Nembutal solution (Vetoquinol). Tissues were immediately excised, washed in ice-cold saline, placed into pre-labelled bags and frozen using a liquid nitrogen-cooled biosqueezer. The bags were then placed in liquid nitrogen until all collections were finished and finally stored at -80°C until further processing. Where necessary tumors were rapidly separated from normal tissue prior to freezing with tumor and normal tissue being stored separately. |
| Sample Type: | Liver |
| Collection Method: | Surgical removal, tissue snap-freezing |
| Storage Conditions: | -80℃ |
Treatment:
| Treatment ID: | TR001777 |
| Treatment Summary: | 2-week old mice were injected i.p. diethylnitrosamine (DEN, 25 mg/Kg) in phosphate buffered saline (3.17 mg/ml). At 6-weeks of age, mice were randomized into two groups: control diet (CD, E15742-33 ssniff Spezialdiäten GmbH) or high fat diet (HFD, S8655-E220 sniff Spezialdiäten GmbH). |
| Treatment Compound: | dietylnitrosamine (DEN) |
| Treatment Route: | i.v. |
| Treatment Dose: | 25mg/kg |
| Treatment Doseduration: | single dose at 2-weeks age |
| Treatment Vehicle: | phosphate buffered saline (PBS) |
| Animal Endp Euthanasia: | 50 µl of 60 mg/ml Nembutal solution (Vetoquinol) |
| Animal Endp Clinical Signs: | 20% increase in abdomen diameter and hard mass detection via palpation, loss of ambulation, loss of skin elasticity, labored respiration, or weight loss over 20 % of initial body weight |
Sample Preparation:
| Sampleprep ID: | SP001770 |
| Sampleprep Summary: | Lipids were extracted from liver samples with 700 μl of sample (100 μl of plasma diluted in PBS, or 700 μl of homogenized cells) was mixed with 800 μl 1 N HCl:CH3OH 1:8 (v/v), 900 μl CHCl3, 200 μg/ml of the antioxidant 2,6-di-tert-butyl-4-methylphenol (BHT; Sigma Aldrich) and 3 μl of SPLASH® LIPIDOMIX® Mass Spec Standard (#330707, Avanti Polar Lipids). After vortexing and centrifugation, the lower organic fraction was collected and evaporated using a Savant Speedvac spd111v (Thermo Fisher Scientific) at room temperature and the remaining lipid pellet was stored at - 20°C under argon. Just before mass spectrometry analysis, lipid pellets were reconstituted in 100% ethanol. |
Combined analysis:
| Analysis ID | AN002754 | AN002755 |
|---|---|---|
| Analysis type | MS | MS |
| Chromatography type | HILIC | HILIC |
| Chromatography system | Shimadzu Nexera X2 | Shimadzu Nexera X2 |
| Column | Waters Xbridge Amide (150 x 4.6mm,3.5um) | Waters Xbridge Amide (150 x 4.6mm,3.5um) |
| MS Type | ESI | ESI |
| MS instrument type | Triple quadrupole | Triple quadrupole |
| MS instrument name | ABI Sciex 6500+ QTrap | ABI Sciex 6500+ QTrap |
| Ion Mode | POSITIVE | NEGATIVE |
| Units | nmol lipid/mg DNA | nmol lipid/mg DNA |
Chromatography:
| Chromatography ID: | CH002035 |
| Instrument Name: | Shimadzu Nexera X2 |
| Column Name: | Waters Xbridge Amide (150 x 4.6mm,3.5um) |
| Chromatography Type: | HILIC |
MS:
| MS ID: | MS002551 |
| Analysis ID: | AN002754 |
| Instrument Name: | ABI Sciex 6500+ QTrap |
| Instrument Type: | Triple quadrupole |
| MS Type: | ESI |
| MS Comments: | - |
| Ion Mode: | POSITIVE |
| MS ID: | MS002552 |
| Analysis ID: | AN002755 |
| Instrument Name: | ABI Sciex 6500+ QTrap |
| Instrument Type: | Triple quadrupole |
| MS Type: | ESI |
| MS Comments: | - |
| Ion Mode: | NEGATIVE |
