Summary of Study ST000257
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 PR000209. The data can be accessed directly via it's Project DOI: 10.21228/M8CP4Q This work is supported by NIH grant, U2C- DK119886.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
Study ID | ST000257 |
Study Title | NIH WCMC Pilot & Feasibility Project: Metabolite changes associated with weight loss |
Study Type | Feeding study |
Study Summary | Targeted metabolomic analyses of oxylipins, endocannabinoids, and ceramides were performed on 18 mouse liver, adipose, hypothalamus, plasma, and muscle samples collected from mice euthanized at 18 weeks following consumption of three diet regimens that induced lean, obese, and weight loss phenotypes. Samples were analyzed by UPLC-MS/MS using a Waters Acquity UPLC and detected on an API 4000 QTrap (AB Sciex, Framingham, MA, USA) by multiple reaction monitoring (MRM) after negative mode electrospray ionization. |
Institute | University of California, Davis |
Department | Nutrition |
Laboratory | Newman Lab |
Last Name | Newman |
First Name | John |
Address | 430 W. Health Sciences Dr., Davis, CA 95616 |
john.newman@ars.usda.gov | |
Phone | +1-530-752-1009 |
Submit Date | 2015-01-16 |
Num Groups | 3 |
Total Subjects | 18 |
Raw Data Available | Yes |
Raw Data File Type(s) | mzML |
Uploaded File Size | 128 MB |
Analysis Type Detail | LC-MS |
Release Date | 2015-09-24 |
Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
Project ID: | PR000209 |
Project DOI: | doi: 10.21228/M8CP4Q |
Project Title: | Metabolite changes associated with weight loss |
Project Type: | Feeding study |
Project Summary: | This study aims to identify changes in metabolites that occur in metabolic tissues, including liver, adipose (epididymal), hypothalamus, and muscle, as well as plsma, in the obese state that are long-lasting and not reversed by weight loss. Mice were divided into three groups termed LFD (low fat diet), HFD (high fat diet), and SW (switch diet from HFD to LFD)(n = 6 per group). All mice were fed normal chow until 12 weeks of age. The LFD group were fed a low fat diet (10% fat) ad libitum for 18 weeks. The HFD diet group were fed high fat diet (60% fat) ad libitum for 18 weeks. The SW group were fed high fat diet for 9 weeks, then low fat diet for 9 weeks after which their body weights returned to similar levels as the LFD group. Each group was analyzed for metabolite and gene expression changes. |
Institute: | University of California, San Diego |
Department: | Department of Medicine |
Laboratory: | Osborn |
Last Name: | Osborn |
First Name: | Olivia |
Address: | 9500 Gilman Dr., La Jolla, CA 92093 |
Email: | oosborn@ucsd.edu |
Phone: | +1-858-822-6645 |
Funding Source: | National Institute of Health U24 DK092993 |
Subject:
Subject ID: | SU000277 |
Subject Type: | Animal |
Subject Species: | Mus musculus |
Taxonomy ID: | 10090 |
Age Or Age Range: | 30 weeks |
Gender: | Female |
Animal Housing: | Singly housed |
Animal Feed: | High fat diet (D12492, Research Diets, New Brunswick, NJ), Low fat diet (D12450, Research Diets, New Brunswick, NJ) |
Species Group: | Mammals |
Factors:
Subject type: Animal; Subject species: Mus musculus (Factor headings shown in green)
mb_sample_id | local_sample_id | Treatment | Tissue Type |
---|---|---|---|
SA011683 | HF epi 2 | HFD | Adipose |
SA011684 | HF epi 3 | HFD | Adipose |
SA011685 | HF epi 4 | HFD | Adipose |
SA011686 | HF epi 7 | HFD | Adipose |
SA011687 | HF epi 1 | HFD | Adipose |
SA011688 | HF epi 8 | HFD | Adipose |
SA011689 | HF Hypo 1 | HFD | Hypothalmus |
SA011690 | HF Hypo 8 | HFD | Hypothalmus |
SA011691 | HF Hypo 4 | HFD | Hypothalmus |
SA011692 | HF Hypo 7 | HFD | Hypothalmus |
SA011693 | HF Hypo 2 | HFD | Hypothalmus |
SA011694 | HF Hypo 3 | HFD | Hypothalmus |
SA011695 | HF liv 7 | HFD | Liver |
SA011696 | HF liv 4 | HFD | Liver |
SA011697 | HF liv 3 | HFD | Liver |
SA011698 | HF liv 2 | HFD | Liver |
SA011699 | HF liv 8 | HFD | Liver |
SA011700 | HF liv 1 | HFD | Liver |
SA011701 | HF mus 4 | HFD | Muscle |
SA011702 | HF mus 2 | HFD | Muscle |
SA011703 | HF mus 3 | HFD | Muscle |
SA011704 | HF mus 7 | HFD | Muscle |
SA011705 | HF mus 8 | HFD | Muscle |
SA011706 | HF mus 1 | HFD | Muscle |
SA011707 | HF plasma 1 | HFD | Plasma |
SA011708 | HF plasma 8 | HFD | Plasma |
SA011709 | HF plasma 7 | HFD | Plasma |
SA011710 | HF plasma 4 | HFD | Plasma |
SA011711 | HF plasma 3 | HFD | Plasma |
SA011712 | HF plasma 2 | HFD | Plasma |
SA011713 | LF epi 3 | LFD | Adipose |
SA011714 | LF epi 7 | LFD | Adipose |
SA011715 | LF epi 2 | LFD | Adipose |
SA011716 | LF epi 1 | LFD | Adipose |
SA011717 | LF epi 8 | LFD | Adipose |
SA011718 | LF epi 6 | LFD | Adipose |
SA011719 | LF Hypo 8 | LFD | Hypothalmus |
SA011720 | LF Hypo 6 | LFD | Hypothalmus |
SA011721 | LF Hypo 7 | LFD | Hypothalmus |
SA011722 | LF Hypo 3 | LFD | Hypothalmus |
SA011723 | LF Hypo 2 | LFD | Hypothalmus |
SA011724 | LF Hypo 1 | LFD | Hypothalmus |
SA011725 | LF liv 3 | LFD | Liver |
SA011726 | LF liv 2 | LFD | Liver |
SA011727 | LF liv 6 | LFD | Liver |
SA011728 | LF liv 8 | LFD | Liver |
SA011729 | LF liv 1 | LFD | Liver |
SA011730 | LF liv 7 | LFD | Liver |
SA011731 | LF mus 3 | LFD | Muscle |
SA011732 | LF mus 7 | LFD | Muscle |
SA011733 | LF mus 6 | LFD | Muscle |
SA011734 | LF mus 1 | LFD | Muscle |
SA011735 | LF mus 8 | LFD | Muscle |
SA011736 | LF mus 2 | LFD | Muscle |
SA011737 | LF plasma 8 | LFD | Plasma |
SA011738 | LF plasma 2 | LFD | Plasma |
SA011739 | LF plasma 7 | LFD | Plasma |
SA011740 | LF plasma 1 | LFD | Plasma |
SA011741 | LF plasma 6 | LFD | Plasma |
SA011742 | LF plasma 3 | LFD | Plasma |
SA011743 | SW epi 3 | SW | Adipose |
SA011744 | SW epi 2 | SW | Adipose |
SA011745 | SW epi 4 | SW | Adipose |
SA011746 | SW epi 8 | SW | Adipose |
SA011747 | SW epi 5 | SW | Adipose |
SA011748 | SW epi 7 | SW | Adipose |
SA011749 | SW Hypo 8 | SW | Hypothalmus |
SA011750 | SW Hypo 7 | SW | Hypothalmus |
SA011751 | SW Hypo 5 | SW | Hypothalmus |
SA011752 | SW Hypo 2 | SW | Hypothalmus |
SA011753 | SW Hypo 3 | SW | Hypothalmus |
SA011754 | SW Hypo 4 | SW | Hypothalmus |
SA011755 | SW liv 3 | SW | Liver |
SA011756 | SW liv 2 | SW | Liver |
SA011757 | SW liv 4 | SW | Liver |
SA011758 | SW liv 5 | SW | Liver |
SA011759 | SW liv 7 | SW | Liver |
SA011760 | SW liv 8 | SW | Liver |
SA011761 | SW mus 5 | SW | Muscle |
SA011762 | SW mus 4 | SW | Muscle |
SA011763 | SW mus 7 | SW | Muscle |
SA011764 | SW mus 2 | SW | Muscle |
SA011765 | SW mus 8 | SW | Muscle |
SA011766 | SW mus 3 | SW | Muscle |
SA011767 | SW plasma 7 | SW | Plasma |
SA011768 | SW plasma 8 | SW | Plasma |
SA011769 | SW plasma 5 | SW | Plasma |
SA011770 | SW plasma 3 | SW | Plasma |
SA011771 | SW plasma 2 | SW | Plasma |
SA011772 | SW plasma 4 | SW | Plasma |
Showing results 1 to 90 of 90 |
Collection:
Collection ID: | CO000269 |
Collection Summary: | - |
Collection Protocol Filename: | NewmanLab-Mediators-Protocol-PT.pdf |
Sample Type: | Liver, adipose, hypothalamus, muscle, and plasma |
Collection Method: | Dissection |
Storage Conditions: | - 80°C |
Storage Vials: | Eppendorf tubes |
Treatment:
Treatment ID: | TR000289 |
Treatment Summary: | Mice were fed 18 weeks on either a low fat diet (LF), high fat diet (HF), or combination of both (SW). |
Treatment Protocol Filename: | NewmanLab-Mediators-Protocol-PT.pdf |
Treatment: | Intervention |
Treatment Doseduration: | 18 weeks |
Treatment Vehicle: | animal feed |
Animal Endp Euthanasia: | 30 weeks |
Animal Endp Tissue Coll List: | Liver, adipose, hypothalami, muscle, and plasma |
Animal Endp Tissue Proc Method: | Dissected, placed on dry ice |
Sample Preparation:
Sampleprep ID: | SP000283 |
Sampleprep Summary: | Tissues were pulverized on dry ice, enriched with deuterated surrogates, antioxidants (BHT and EDTA), and extracted with MeOH:Water:IPA, transferred to an Ostro plate and the extract was eluted by vacuum. Plasma was added directly to the plate, mixed with the surrogates, antioxidants, and IPA and the extract eluted through. The extracts were dried, reconstituted in 100?L 50:50 methanol:acetonitrile with internal standards 1?phenyl?3?hexanoic acid urea and 1?cyclohexyl?3-dodecanoic acid urea (Sigma-Aldrich, St. Louis, MO) and filtered at 0.1 µm. |
Sampleprep Protocol Filename: | NewmanLab-Mediators-Protocol-PT.pdf |
Extraction Method: | Ostro plate |
Extract Concentration Dilution: | 80 µL |
Extract Cleanup: | Ostro plate |
Extract Storage: | - 20 °C |
Sample Resuspension: | 100 µL |
Sample Spiking: | See sample prep protocol file |
Organ: | Liver, adipose, hypothalamus, muscle, and plasma |
Combined analysis:
Analysis ID | AN000406 | AN000407 | AN000408 |
---|---|---|---|
Analysis type | MS | MS | MS |
Chromatography type | |||
Chromatography system | Waters Acquity | Waters Acquity | Waters Acquity |
Column | |||
MS Type | ESI | ESI | ESI |
MS instrument type | Triple quadrupole | Triple quadrupole | Triple quadrupole |
MS instrument name | ABI Sciex API 4000 QTrap | ABI Sciex API 4000 QTrap | ABI Sciex API 4000 QTrap |
Ion Mode | NEGATIVE | POSITIVE | POSITIVE |
Units | % Area Ratio | nM | nM |
Chromatography:
Chromatography ID: | CH000287 |
Chromatography Summary: | Oxylipin analysis |
Methods Filename: | NewmanLab-Mediators-Protocol-PT.pdf |
Instrument Name: | Waters Acquity |
Column Temperature: | 60 C |
Flow Gradient: | See protocol/methods file |
Flow Rate: | 0.25 |
Internal Standard: | See protocol/methods file |
Retention Time: | See protocol/methods file |
Sample Injection: | 5 L |
Solvent A: | 100% water; 0.1% acetic acid |
Solvent B: | 90% acetonitrile/ 10% isopropanol |
Analytical Time: | 16 min |
Weak Wash Solvent Name: | 20% methanol, 10% isopropanol |
Weak Wash Volume: | 600 L |
Strong Wash Solvent Name: | 50:50 Acetonitrile:Methanol |
Strong Wash Volume: | 600 L |
Sample Loop Size: | 17 L |
Chromatography ID: | CH000288 |
Chromatography Summary: | Endocannabinoid analysis |
Methods Filename: | NewmanLab-Mediators-Protocol-PT.pdf |
Instrument Name: | Waters Acquity |
Column Temperature: | 60 C |
Flow Gradient: | See protocol/methods file |
Flow Rate: | 0.25 |
Internal Standard: | See protocol/methods file |
Retention Time: | See protocol/methods file |
Sample Injection: | 5 L |
Solvent A: | 100% water; 0.1% acetic acid |
Solvent B: | 90% acetonitrile/ 10% isopropanol |
Analytical Time: | 11 min |
Weak Wash Solvent Name: | 20% methanol, 10% isopropanol |
Weak Wash Volume: | 600 L |
Strong Wash Solvent Name: | 50:50 Acetonitrile:Methanol |
Strong Wash Volume: | 600 L |
Sample Loop Size: | 17 L |
Chromatography ID: | CH000289 |
Chromatography Summary: | Ceramide analysis |
Methods Filename: | NewmanLab-Mediators-Protocol-PT.pdf |
Instrument Name: | Waters Acquity |
Column Temperature: | 60 C |
Flow Gradient: | See protocol/methods file |
Flow Rate: | 0.25 |
Internal Standard: | See protocol/methods file |
Retention Time: | See protocol/methods file |
Sample Injection: | 5 L |
Solvent A: | 100% water; 5 mM ammonium formate; 0.2% formic acid |
Solvent B: | 100% methanol; 0.2% formic acid; 5 mM ammonium formate |
Analytical Time: | 15 min |
Weak Wash Solvent Name: | 20% methanol, 10% isopropanol |
Weak Wash Volume: | 600 L |
Strong Wash Solvent Name: | 50:50 Acetonitrile:Methanol |
Strong Wash Volume: | 600 L |
Sample Loop Size: | 17 L |
MS:
MS ID: | MS000348 |
Analysis ID: | AN000406 |
Instrument Name: | ABI Sciex API 4000 QTrap |
Instrument Type: | Triple quadrupole |
MS Type: | ESI |
MS Comments: | See protocol file |
Ion Mode: | NEGATIVE |
MS ID: | MS000349 |
Analysis ID: | AN000407 |
Instrument Name: | ABI Sciex API 4000 QTrap |
Instrument Type: | Triple quadrupole |
MS Type: | ESI |
MS Comments: | See protocol file |
Ion Mode: | POSITIVE |
MS ID: | MS000350 |
Analysis ID: | AN000408 |
Instrument Name: | ABI Sciex API 4000 QTrap |
Instrument Type: | Triple quadrupole |
MS Type: | ESI |
MS Comments: | See protocol file |
Ion Mode: | POSITIVE |