Summary of Study ST001346

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 PR000917. The data can be accessed directly via it's Project DOI: 10.21228/M8568J This work is supported by NIH grant, U2C- DK119886.

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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 IDST001346
Study TitleMetabolomic changes in mouse liver on a protein restricted diet (part-I)
Study SummaryThe data provided here are in support of the publication “Restriction of essential amino acids dictates the systemic metabolic response to dietary protein dilution” Yann W. Yap et al. Nature Communications 2020 (accepted for publication). Here we provide untargeted metabolomics LC-MS data from liver from C57Bl/6NCrl mice fed a diet in which dietary protein was restricted and corresponding unrestricted controls. Specifically, liver from animals on a low-protein diet following a week of diet adaptation and correspond controls with n = 5 for each group.
Institute
Monash University
DepartmentDepartment of Biochemistry and Molecular Biology
LaboratoryNutrient Metabolism and Signalling Laboratory
Last NameRose
First NameAdam
AddressMonash University, Clayton Campus, 23 Innovation Walk, Clayton, Victoria, 3800, Australia
Emailadam.rose@monash.edu
Phone+61 3 99029340
Submit Date2020-04-01
Num Groups2
Total Subjects10
Num Males10
Study CommentsStudy 1 of 3 for this project
Raw Data AvailableYes
Raw Data File Type(s)raw(Thermo)
Analysis Type DetailLC-MS
Release Date2020-07-20
Release Version1
Adam Rose Adam Rose
https://dx.doi.org/10.21228/M8568J
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR000917
Project DOI:doi: 10.21228/M8568J
Project Title:Restriction of essential amino acids dictates the systemic metabolic response to dietary protein dilution
Project Summary:The data provided here are in support of the publication “Restriction of essential amino acids dictates the systemic metabolic response to dietary protein dilution” Yann W. Yap et al. Nature Communications 2020 (accepted for publication). Here we provide untargeted metabolomics LC-MS data from liver and plasma from mice fed a diet in which dietary protein was restricted and corresponding unrestricted controls. Specifically, part 1 and 2 correspond to liver and plasma from the hepatic portal vein respectively from animals on a low-protein diet following a week of diet adaptation and correspond controls with n = 5 for each group. Part 3 of the data presented here corresponds to liver from mice subject to a 3wk treatment with diets either containing 18% digestible energy from amino acids or a diet with restricted amounts of threonine and following prior treatments with adeno-associated viruses to transduce the liver to express yeast threonine biosynthetic enzymes (AAV-yTHR1+THR4) or a negative control (AAV-GFP). n= 6 individual mice per group.
Institute:Monash University
Department:Department of Biochemistry and Molecular Biology
Laboratory:Nutrient Metabolism and Signalling Laboratory
Last Name:Rose
First Name:Adam
Address:Monash University, Clayton Campus, 23 Innovation Walk, Clayton, Victoria, 3800, Australia
Email:adam.rose@monash.edu
Phone:+61 3 99029340

Subject:

Subject ID:SU001420
Subject Type:Mammal
Subject Species:Mus musculus
Taxonomy ID:10090
Genotype Strain:C57Bl/6NCrl
Age Or Age Range:7 to 10 weeks
Gender:Male
Animal Animal Supplier:Charles River Laboratories, DEU
Animal Light Cycle:12-12h light-dark cycle

Factors:

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

mb_sample_id local_sample_id Diet
SA097856AR101_1-1Control (normal protein diet) D12450B
SA097857AR105_1-5Control (normal protein diet) D12450B
SA097858AR104_1-4Control (normal protein diet) D12450B
SA097859AR102_1-2Control (normal protein diet) D12450B
SA097860AR103_1-3Control (normal protein diet) D12450B
SA097861AR110_2-5Reduced protein diet D10062201
SA097862AR109_2-4Reduced protein diet D10062201
SA097863AR106_2-1Reduced protein diet D10062201
SA097864AR107_2-2Reduced protein diet D10062201
SA097865AR108_2-3Reduced protein diet D10062201
Showing results 1 to 10 of 10

Collection:

Collection ID:CO001415
Collection Summary:Mice were fasted overnight and then re-fed for 5 to 6 hours before being humanely euthanised for tissue collection.
Sample Type:Liver
Storage Conditions:-80℃

Treatment:

Treatment ID:TR001435
Treatment Summary:Male mice aged 7 weeks upon arrival, were acclimated to the local housing facility (12-12h light-dark cycle, 22-24°C) for one week prior to experimentation and were fed standard rodent chow (3437, Provimi Kliba, DEU). Following acclimation, mice were placed on either a normal protein diet (D12450B, Research Diets, New Jersey, USA) or a reduced protein diet (D10062201, Research Diets, New Jersey, USA) for 3 weeks prior to being humanely euthanised for tissue collection.

Sample Preparation:

Sampleprep ID:SP001428
Sampleprep Summary:Livers were cryogenically pulverized (cryopulverization) using a 12-well biopulverizer (BioSpec Products, OK USA Part number 59012MS) according to the manufacturer’s instructions. The frozen tissue powder was then weighed and extracted in 20 µL of extraction solvent (0°C) per mg of tissue. The mixture was then briefly vortexed before sonication in an ice-water bath for 10 minutes followed by centrifugation (20,000 rcf, 4℃, 10 minutes). The supernatant was then transferred to a mass spectrometry vial for LC-MS analysis. The extraction solvent consisted of 2:6:1 CHCl3:MeOH:H2O v/v/v with 2 µM CHAPS, CAPS, PIPES and TRIS as internal standards.
Processing Storage Conditions:Described in summary
Extract Storage:-80℃

Combined analysis:

Analysis ID AN002240
Analysis type MS
Chromatography type HILIC
Chromatography system Thermo Dionex Ultimate 3000 RS
Column SeQuant ZIC-pHILIC (150 x 4.6mm,5um)
MS Type ESI
MS instrument type Orbitrap
MS instrument name Thermo Q Exactive Orbitrap
Ion Mode UNSPECIFIED
Units Peak Area

Chromatography:

Chromatography ID:CH001646
Chromatography Summary:Chromatography utilized a ZIC-pHILIC column (column temperature 25 °C) with a gradient elution of 20 mM ammonium carbonate (A) and acetonitrile (B) (linear gradient time-%B as follows: 0 min-80%, 15 min-50%, 18 min-5%, 21 min-5%, 24 min-80%, 32 min-80%) on a Dionex RSLC3000 UHPLC (Thermo). The flow rate was maintained at 300 μL/min. Samples were kept at 4 °C in the autosampler and 10 μL injected for analysis.
Instrument Name:Thermo Dionex Ultimate 3000 RS
Column Name:SeQuant ZIC-pHILIC (150 x 4.6mm,5um)
Column Temperature:25
Flow Gradient:linear gradient time-%B as follows: 0 min-80%, 15 min-50%, 18 min-5%, 21 min-5%, 24 min-80%, 32 min-80%
Flow Rate:300 µL/min
Solvent A:100% water; 20 mM ammonium carbonate
Solvent B:100% water; acetonitrile
Chromatography Type:HILIC

MS:

MS ID:MS002086
Analysis ID:AN002240
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:Mass spectrometry was performed at 35 000 resolution (accuracy calibrated to <1 ppm) on a Q-Exactive Orbitrap MS (Thermo) operating in rapid switching positive (4 kV) and negative (−3.5 kV) mode electrospray ionization (capillary temperature 300 °C; sheath gas 50; Aux gas 20; sweep gas 2; probe temp 120 °C).
Ion Mode:UNSPECIFIED
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