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.

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Study IDST000257
Study TitleNIH WCMC Pilot & Feasibility Project: “Metabolite changes associated with weight loss”
Study TypeFeeding study
Study SummaryTargeted 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
DepartmentNutrition
LaboratoryNewman Lab
Last NameNewman
First NameJohn
Address430 W. Health Sciences Dr., Davis, CA 95616
Emailjohn.newman@ars.usda.gov
Phone+1-530-752-1009
Submit Date2015-01-16
Num Groups3
Total Subjects18
Raw Data AvailableYes
Raw Data File Type(s)mzML
Uploaded File Size128 MB
Analysis Type DetailLC-MS
Release Date2015-09-24
Release Version1
John Newman John Newman
https://dx.doi.org/10.21228/M8CP4Q
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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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:Mammal

Factors:

Subject type: Animal; Subject species: Mus musculus (Factor headings shown in green)

mb_sample_id local_sample_id Treatment Tissue Type
SA011683HF epi 2HFD Adipose
SA011684HF epi 3HFD Adipose
SA011685HF epi 4HFD Adipose
SA011686HF epi 7HFD Adipose
SA011687HF epi 1HFD Adipose
SA011688HF epi 8HFD Adipose
SA011689HF Hypo 1HFD Hypothalmus
SA011690HF Hypo 8HFD Hypothalmus
SA011691HF Hypo 4HFD Hypothalmus
SA011692HF Hypo 7HFD Hypothalmus
SA011693HF Hypo 2HFD Hypothalmus
SA011694HF Hypo 3HFD Hypothalmus
SA011695HF liv 7HFD Liver
SA011696HF liv 4HFD Liver
SA011697HF liv 3HFD Liver
SA011698HF liv 2HFD Liver
SA011699HF liv 8HFD Liver
SA011700HF liv 1HFD Liver
SA011701HF mus 4HFD Muscle
SA011702HF mus 2HFD Muscle
SA011703HF mus 3HFD Muscle
SA011704HF mus 7HFD Muscle
SA011705HF mus 8HFD Muscle
SA011706HF mus 1HFD Muscle
SA011707HF plasma 1HFD Plasma
SA011708HF plasma 8HFD Plasma
SA011709HF plasma 7HFD Plasma
SA011710HF plasma 4HFD Plasma
SA011711HF plasma 3HFD Plasma
SA011712HF plasma 2HFD Plasma
SA011713LF epi 3LFD Adipose
SA011714LF epi 7LFD Adipose
SA011715LF epi 2LFD Adipose
SA011716LF epi 1LFD Adipose
SA011717LF epi 8LFD Adipose
SA011718LF epi 6LFD Adipose
SA011719LF Hypo 8LFD Hypothalmus
SA011720LF Hypo 6LFD Hypothalmus
SA011721LF Hypo 7LFD Hypothalmus
SA011722LF Hypo 3LFD Hypothalmus
SA011723LF Hypo 2LFD Hypothalmus
SA011724LF Hypo 1LFD Hypothalmus
SA011725LF liv 3LFD Liver
SA011726LF liv 2LFD Liver
SA011727LF liv 6LFD Liver
SA011728LF liv 8LFD Liver
SA011729LF liv 1LFD Liver
SA011730LF liv 7LFD Liver
SA011731LF mus 3LFD Muscle
SA011732LF mus 7LFD Muscle
SA011733LF mus 6LFD Muscle
SA011734LF mus 1LFD Muscle
SA011735LF mus 8LFD Muscle
SA011736LF mus 2LFD Muscle
SA011737LF plasma 8LFD Plasma
SA011738LF plasma 2LFD Plasma
SA011739LF plasma 7LFD Plasma
SA011740LF plasma 1LFD Plasma
SA011741LF plasma 6LFD Plasma
SA011742LF plasma 3LFD Plasma
SA011743SW epi 3SW Adipose
SA011744SW epi 2SW Adipose
SA011745SW epi 4SW Adipose
SA011746SW epi 8SW Adipose
SA011747SW epi 5SW Adipose
SA011748SW epi 7SW Adipose
SA011749SW Hypo 8SW Hypothalmus
SA011750SW Hypo 7SW Hypothalmus
SA011751SW Hypo 5SW Hypothalmus
SA011752SW Hypo 2SW Hypothalmus
SA011753SW Hypo 3SW Hypothalmus
SA011754SW Hypo 4SW Hypothalmus
SA011755SW liv 3SW Liver
SA011756SW liv 2SW Liver
SA011757SW liv 4SW Liver
SA011758SW liv 5SW Liver
SA011759SW liv 7SW Liver
SA011760SW liv 8SW Liver
SA011761SW mus 5SW Muscle
SA011762SW mus 4SW Muscle
SA011763SW mus 7SW Muscle
SA011764SW mus 2SW Muscle
SA011765SW mus 8SW Muscle
SA011766SW mus 3SW Muscle
SA011767SW plasma 7SW Plasma
SA011768SW plasma 8SW Plasma
SA011769SW plasma 5SW Plasma
SA011770SW plasma 3SW Plasma
SA011771SW plasma 2SW Plasma
SA011772SW plasma 4SW 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
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