{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST001348","ANALYSIS_ID":"AN002242","VERSION":"1","CREATED_ON":"02-08-2024"},

"PROJECT":{"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","DOI":"http://dx.doi.org/10.21228/M8568J"},

"STUDY":{"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","EMAIL":"adam.rose@monash.edu","PHONE":"+61 3 99029340","SUBMIT_DATE":"2020-04-03"},

"SUBJECT":{"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"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"-",
"Sample ID":"AR401_control_AA_GFP_1pt1",
"Factors":{"Diet":"Control diet SF17-177","Virus treatment":"AAV-GFP"},
"Additional sample data":{"RAW_FILE_NAME":"C120181105_AR401_control_AA_GFP_1pt1_1.raw"}
},
{
"Subject ID":"-",
"Sample ID":"AR402_control_AA_GFP_1pt2",
"Factors":{"Diet":"Control diet SF17-177","Virus treatment":"AAV-GFP"},
"Additional sample data":{"RAW_FILE_NAME":"C120181105_AR402_control_AA_GFP_1pt2_1.raw"}
},
{
"Subject ID":"-",
"Sample ID":"AR403_control_AA_GFP_1pt3",
"Factors":{"Diet":"Control diet SF17-177","Virus treatment":"AAV-GFP"},
"Additional sample data":{"RAW_FILE_NAME":"C120181105_AR403_control_AA_GFP_1pt3_1.raw"}
},
{
"Subject ID":"-",
"Sample ID":"AR404_control_AA_GFP_2pt1",
"Factors":{"Diet":"Control diet SF17-177","Virus treatment":"AAV-GFP"},
"Additional sample data":{"RAW_FILE_NAME":"C120181105_AR404_control_AA_GFP_2pt1_1.raw"}
},
{
"Subject ID":"-",
"Sample ID":"AR405_control_AA_GFP_2pt2",
"Factors":{"Diet":"Control diet SF17-177","Virus treatment":"AAV-GFP"},
"Additional sample data":{"RAW_FILE_NAME":"C120181105_AR405_control_AA_GFP_2pt2_1.raw"}
},
{
"Subject ID":"-",
"Sample ID":"AR406_control_AA_GFP_2pt3",
"Factors":{"Diet":"Control diet SF17-177","Virus treatment":"AAV-GFP"},
"Additional sample data":{"RAW_FILE_NAME":"C120181105_AR406_control_AA_GFP_2pt3_1.raw"}
},
{
"Subject ID":"-",
"Sample ID":"AR407_control_AA_THR1plus4_3pt1",
"Factors":{"Diet":"Control diet SF17-177","Virus treatment":"AAV-yTHR1+THR4"},
"Additional sample data":{"RAW_FILE_NAME":"C120181105_AR407_control_AA_THR1plus4_3pt1_1.raw"}
},
{
"Subject ID":"-",
"Sample ID":"AR408_control_AA_THR1plus4_3pt2",
"Factors":{"Diet":"Control diet SF17-177","Virus treatment":"AAV-yTHR1+THR4"},
"Additional sample data":{"RAW_FILE_NAME":"C120181105_AR408_control_AA_THR1plus4_3pt2_1.raw"}
},
{
"Subject ID":"-",
"Sample ID":"AR409_control_AA_THR1plus4_3pt3",
"Factors":{"Diet":"Control diet SF17-177","Virus treatment":"AAV-yTHR1+THR4"},
"Additional sample data":{"RAW_FILE_NAME":"C120181105_AR409_control_AA_THR1plus4_3pt3_1.raw"}
},
{
"Subject ID":"-",
"Sample ID":"AR410_control_AA_THR1plus4_4pt1",
"Factors":{"Diet":"Control diet SF17-177","Virus treatment":"AAV-yTHR1+THR4"},
"Additional sample data":{"RAW_FILE_NAME":"C120181105_AR410_control_AA_THR1plus4_4pt1_1.raw"}
},
{
"Subject ID":"-",
"Sample ID":"AR411_control_AA_THR1plus4_4pt2",
"Factors":{"Diet":"Control diet SF17-177","Virus treatment":"AAV-yTHR1+THR4"},
"Additional sample data":{"RAW_FILE_NAME":"C120181105_AR411_control_AA_THR1plus4_4pt2_1.raw"}
},
{
"Subject ID":"-",
"Sample ID":"AR412_control_AA_THR1plus4_4pt3",
"Factors":{"Diet":"Control diet SF17-177","Virus treatment":"AAV-yTHR1+THR4"},
"Additional sample data":{"RAW_FILE_NAME":"C120181105_AR412_control_AA_THR1plus4_4pt3_1.raw"}
},
{
"Subject ID":"-",
"Sample ID":"AR413_Low_T_GFP_5pt1",
"Factors":{"Diet":"Low Threonine diet SF18-066","Virus treatment":"AAV-GFP"},
"Additional sample data":{"RAW_FILE_NAME":"C120181105_AR413_Low_T_GFP_5pt1_1.raw"}
},
{
"Subject ID":"-",
"Sample ID":"AR414_Low_T_GFP_5pt2",
"Factors":{"Diet":"Low Threonine diet SF18-066","Virus treatment":"AAV-GFP"},
"Additional sample data":{"RAW_FILE_NAME":"C120181105_AR414_Low_T_GFP_5pt2_1.raw"}
},
{
"Subject ID":"-",
"Sample ID":"AR415_Low_T_GFP_5pt3",
"Factors":{"Diet":"Low Threonine diet SF18-066","Virus treatment":"AAV-GFP"},
"Additional sample data":{"RAW_FILE_NAME":"C120181105_AR415_Low_T_GFP_5pt3_1.raw"}
},
{
"Subject ID":"-",
"Sample ID":"AR416_Low_T_GFP_6pt1",
"Factors":{"Diet":"Low Threonine diet SF18-066","Virus treatment":"AAV-GFP"},
"Additional sample data":{"RAW_FILE_NAME":"C120181105_AR416_Low_T_GFP_6pt1_1.raw"}
},
{
"Subject ID":"-",
"Sample ID":"AR417_Low_T_GFP_6pt2",
"Factors":{"Diet":"Low Threonine diet SF18-066","Virus treatment":"AAV-GFP"},
"Additional sample data":{"RAW_FILE_NAME":"C120181105_AR417_Low_T_GFP_6pt2_1.raw"}
},
{
"Subject ID":"-",
"Sample ID":"AR418_Low_T_GFP_6pt3",
"Factors":{"Diet":"Low Threonine diet SF18-066","Virus treatment":"AAV-GFP"},
"Additional sample data":{"RAW_FILE_NAME":"C120181105_AR418_Low_T_GFP_6pt3_1.raw"}
},
{
"Subject ID":"-",
"Sample ID":"AR419_Low_T_THR1plus4_7pt1",
"Factors":{"Diet":"Low Threonine diet SF18-066","Virus treatment":"AAV-yTHR1+THR4"},
"Additional sample data":{"RAW_FILE_NAME":"C120181105_AR419_Low_T_THR1plus4_7pt1_1.raw"}
},
{
"Subject ID":"-",
"Sample ID":"AR420_Low_T_THR1plus4_7pt2",
"Factors":{"Diet":"Low Threonine diet SF18-066","Virus treatment":"AAV-yTHR1+THR4"},
"Additional sample data":{"RAW_FILE_NAME":"C120181105_AR420_Low_T_THR1plus4_7pt2_1.raw"}
},
{
"Subject ID":"-",
"Sample ID":"AR421_Low_T_THR1plus4_7pt3",
"Factors":{"Diet":"Low Threonine diet SF18-066","Virus treatment":"AAV-yTHR1+THR4"},
"Additional sample data":{"RAW_FILE_NAME":"C120181105_AR421_Low_T_THR1plus4_7pt3_1.raw"}
},
{
"Subject ID":"-",
"Sample ID":"AR422_Low_T_THR1plus4_8pt1",
"Factors":{"Diet":"Low Threonine diet SF18-066","Virus treatment":"AAV-yTHR1+THR4"},
"Additional sample data":{"RAW_FILE_NAME":"C120181105_AR422_Low_T_THR1plus4_8pt1_1.raw"}
},
{
"Subject ID":"-",
"Sample ID":"AR423_Low_T_THR1plus4_8pt2",
"Factors":{"Diet":"Low Threonine diet SF18-066","Virus treatment":"AAV-yTHR1+THR4"},
"Additional sample data":{"RAW_FILE_NAME":"C120181105_AR423_Low_T_THR1plus4_8pt2_1.raw"}
},
{
"Subject ID":"-",
"Sample ID":"AR424_Low_T_THR1plus4_8pt3",
"Factors":{"Diet":"Low Threonine diet SF18-066","Virus treatment":"AAV-yTHR1+THR4"},
"Additional sample data":{"RAW_FILE_NAME":"C120181105_AR424_Low_T_THR1plus4_8pt3_1.raw"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"Mice were humanely euthanised for tissue collection","SAMPLE_TYPE":"Liver","STORAGE_CONDITIONS":"-80℃"},

"TREATMENT":{"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)."},

"SAMPLEPREP":{"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℃"},

"CHROMATOGRAPHY":{"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"},

"ANALYSIS":{"ANALYSIS_TYPE":"MS"},

"MS":{"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","MS_RESULTS_FILE":"ST001348_AN002242_Results.txt UNITS:Peak Area Has RT:Yes RT units:Minutes"}

}