Summary of Study ST001348

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.

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.

Show all samples  |  Perform analysis on untargeted data  
Download mwTab file (text)   |  Download mwTab file(JSON)   |  Download data files (Contains raw data)
Study IDST001348
Study TitleMetabolomic changes in mouse liver on a threonine restricted diet (part-III)
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). The data in this study corresponds to liver from C57Bl/6JMarp mice subject to a 3wk treatment with diets either containing 18% digestible energy from amino acids with either a normal distribution of amino acids or with restricted amounts of threonine. This followed prior treatment 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
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 Date2020-04-03
Num Groups4
Total Subjects24
Num Males24
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

Select appropriate tab below to view additional metadata details:


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:SU001422
Subject Type:Mammal
Subject Species:Mus musculus
Taxonomy ID:10090
Genotype Strain:C57Bl/6JMarp
Age Or Age Range:7 to 12 weeks
Gender:Male
Animal Animal Supplier:Monash University Animal Research Platform, Clayton, AUS

Factors:

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

mb_sample_id local_sample_id Diet Virus treatment
SA097876AR401_control_AA_GFP_1pt1Control diet SF17-177 AAV-GFP
SA097877AR406_control_AA_GFP_2pt3Control diet SF17-177 AAV-GFP
SA097878AR405_control_AA_GFP_2pt2Control diet SF17-177 AAV-GFP
SA097879AR402_control_AA_GFP_1pt2Control diet SF17-177 AAV-GFP
SA097880AR403_control_AA_GFP_1pt3Control diet SF17-177 AAV-GFP
SA097881AR404_control_AA_GFP_2pt1Control diet SF17-177 AAV-GFP
SA097882AR412_control_AA_THR1plus4_4pt3Control diet SF17-177 AAV-yTHR1+THR4
SA097883AR411_control_AA_THR1plus4_4pt2Control diet SF17-177 AAV-yTHR1+THR4
SA097884AR408_control_AA_THR1plus4_3pt2Control diet SF17-177 AAV-yTHR1+THR4
SA097885AR407_control_AA_THR1plus4_3pt1Control diet SF17-177 AAV-yTHR1+THR4
SA097886AR410_control_AA_THR1plus4_4pt1Control diet SF17-177 AAV-yTHR1+THR4
SA097887AR409_control_AA_THR1plus4_3pt3Control diet SF17-177 AAV-yTHR1+THR4
SA097888AR418_Low_T_GFP_6pt3Low Threonine diet SF18-066 AAV-GFP
SA097889AR417_Low_T_GFP_6pt2Low Threonine diet SF18-066 AAV-GFP
SA097890AR413_Low_T_GFP_5pt1Low Threonine diet SF18-066 AAV-GFP
SA097891AR416_Low_T_GFP_6pt1Low Threonine diet SF18-066 AAV-GFP
SA097892AR414_Low_T_GFP_5pt2Low Threonine diet SF18-066 AAV-GFP
SA097893AR415_Low_T_GFP_5pt3Low Threonine diet SF18-066 AAV-GFP
SA097894AR424_Low_T_THR1plus4_8pt3Low Threonine diet SF18-066 AAV-yTHR1+THR4
SA097895AR423_Low_T_THR1plus4_8pt2Low Threonine diet SF18-066 AAV-yTHR1+THR4
SA097896AR421_Low_T_THR1plus4_7pt3Low Threonine diet SF18-066 AAV-yTHR1+THR4
SA097897AR419_Low_T_THR1plus4_7pt1Low Threonine diet SF18-066 AAV-yTHR1+THR4
SA097898AR420_Low_T_THR1plus4_7pt2Low Threonine diet SF18-066 AAV-yTHR1+THR4
SA097899AR422_Low_T_THR1plus4_8pt1Low Threonine diet SF18-066 AAV-yTHR1+THR4
Showing results 1 to 24 of 24

Collection:

Collection ID:CO001417
Collection Summary:Mice were humanely euthanised for tissue collection
Sample Type:Liver
Storage Conditions:-80℃

Treatment:

Treatment ID:TR001437
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 (8720610, Barastoc, AUS). Following acclimation, mice were administered a total of 5E+11 virus particles per mouse via the tail vein. For the negative control (NC): 5E+11 GFP-AAV; and for the THR1/4 overexpression studies mice were administered 2.5E+11 virus particles each of yTHR1-AAV and yTHR4-AAV. One week following this time, the dietary intervention was initiated. In these studies, the low threonine diet (SF18-066, Specialty Feeds AUS) contained homoserine, the substrate of THR1. The corresponding control diet was SF17-177 (Specialty Feeds AUS).

Sample Preparation:

Sampleprep ID:SP001430
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. Additionally where quantitative amino acid analysis was performed, a mixture of 17 stable isotope labelled amino acids (Gln, Asn and Trp were absent) were added at a concentration of 500 pmol of each amino acid per mg liver (Cambridge Isotope Laboratories PN MSK-A2-1.2).
Processing Storage Conditions:Described in summary
Extract Storage:-80℃

Combined analysis:

Analysis ID AN002242
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:CH001648
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:MS002088
Analysis ID:AN002242
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
  logo