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.

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Study IDST001687
Study TitleNon-transformed cells respond to fat by inducing glucose metabolism
Study SummaryC57BL/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
DepartmentDepartment of Oncology
LaboratoryLaboratory of Cellular Metabolism and Metabolic Regulation
Last NameFendt
First NameSarah-Maria
AddressON IV Herestraat 49 - box 912 3000 Leuven
Emailsarah-maria.fendt@kuleuven.be
Phone+32 16 37 32 61
Submit Date2021-02-04
Num Groups4
Total Subjects16
Num Males16
Raw Data AvailableYes
Raw Data File Type(s).mzXML
Analysis Type DetailLC-MS
Release Date2021-02-27
Release Version1
Sarah-Maria Fendt Sarah-Maria Fendt
https://dx.doi.org/10.21228/M8FT4Q
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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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
SA155491CD-PBS_3.1.2Liver CD No
SA155492CD-PBS_3.2.3Liver CD No
SA155493CD-PBS_3.2.1Liver CD No
SA155494CD-PBS_3.1.4Liver CD No
SA155495HFD-PBS_3.5.3Liver HFD No
SA155496HFD-PBS_3.4.4Liver HFD No
SA155497HFD-PBS_3.4.3Liver HFD No
SA155498HFD-PBS_3.5.1Liver HFD No
SA155499HFD-DEN_3D20.2LLiver HFD Yes
SA155500HFD-DEN_3D20.1LLiver HFD Yes
SA155501HFD-DEN_3D19.1LLiver HFD Yes
SA155502HFD-DEN_3D19.2LLiver HFD Yes
SA155503HFD-DEN_3D19.1TTumor HFD Yes
SA155504HFD-DEN_3D20.2TTumor HFD Yes
SA155505HFD-DEN_3D19.2TTumor HFD Yes
SA155506HFD-DEN_3D20.1TTumor 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
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