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.
| Study ID | ST001348 |
| Study Title | Metabolomic changes in mouse liver on a threonine restricted diet (part-III) |
| Study 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). 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 |
| 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 |
| adam.rose@monash.edu | |
| Phone | +61 3 99029340 |
| Submit Date | 2020-04-03 |
| Num Groups | 4 |
| Total Subjects | 24 |
| Num Males | 24 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | raw(Thermo) |
| Analysis Type Detail | LC-MS |
| Release Date | 2020-07-20 |
| Release Version | 1 |
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 |
|---|---|---|---|
| SA097876 | AR401_control_AA_GFP_1pt1 | Control diet SF17-177 | AAV-GFP |
| SA097877 | AR406_control_AA_GFP_2pt3 | Control diet SF17-177 | AAV-GFP |
| SA097878 | AR405_control_AA_GFP_2pt2 | Control diet SF17-177 | AAV-GFP |
| SA097879 | AR402_control_AA_GFP_1pt2 | Control diet SF17-177 | AAV-GFP |
| SA097880 | AR403_control_AA_GFP_1pt3 | Control diet SF17-177 | AAV-GFP |
| SA097881 | AR404_control_AA_GFP_2pt1 | Control diet SF17-177 | AAV-GFP |
| SA097882 | AR412_control_AA_THR1plus4_4pt3 | Control diet SF17-177 | AAV-yTHR1+THR4 |
| SA097883 | AR411_control_AA_THR1plus4_4pt2 | Control diet SF17-177 | AAV-yTHR1+THR4 |
| SA097884 | AR408_control_AA_THR1plus4_3pt2 | Control diet SF17-177 | AAV-yTHR1+THR4 |
| SA097885 | AR407_control_AA_THR1plus4_3pt1 | Control diet SF17-177 | AAV-yTHR1+THR4 |
| SA097886 | AR410_control_AA_THR1plus4_4pt1 | Control diet SF17-177 | AAV-yTHR1+THR4 |
| SA097887 | AR409_control_AA_THR1plus4_3pt3 | Control diet SF17-177 | AAV-yTHR1+THR4 |
| SA097888 | AR418_Low_T_GFP_6pt3 | Low Threonine diet SF18-066 | AAV-GFP |
| SA097889 | AR417_Low_T_GFP_6pt2 | Low Threonine diet SF18-066 | AAV-GFP |
| SA097890 | AR413_Low_T_GFP_5pt1 | Low Threonine diet SF18-066 | AAV-GFP |
| SA097891 | AR416_Low_T_GFP_6pt1 | Low Threonine diet SF18-066 | AAV-GFP |
| SA097892 | AR414_Low_T_GFP_5pt2 | Low Threonine diet SF18-066 | AAV-GFP |
| SA097893 | AR415_Low_T_GFP_5pt3 | Low Threonine diet SF18-066 | AAV-GFP |
| SA097894 | AR424_Low_T_THR1plus4_8pt3 | Low Threonine diet SF18-066 | AAV-yTHR1+THR4 |
| SA097895 | AR423_Low_T_THR1plus4_8pt2 | Low Threonine diet SF18-066 | AAV-yTHR1+THR4 |
| SA097896 | AR421_Low_T_THR1plus4_7pt3 | Low Threonine diet SF18-066 | AAV-yTHR1+THR4 |
| SA097897 | AR419_Low_T_THR1plus4_7pt1 | Low Threonine diet SF18-066 | AAV-yTHR1+THR4 |
| SA097898 | AR420_Low_T_THR1plus4_7pt2 | Low Threonine diet SF18-066 | AAV-yTHR1+THR4 |
| SA097899 | AR422_Low_T_THR1plus4_8pt1 | Low 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 |
