{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST001347","ANALYSIS_ID":"AN002241","VERSION":"1","CREATED_ON":"April 5, 2020, 5:40 pm"},

"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"},

"STUDY":{"STUDY_TITLE":"Metabolomic changes in mouse plasma on a protein restricted diet","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). Here we provide untargeted metabolomics LC-MS data from plasma from C57Bl/6NCrl mice fed a diet in which dietary protein was restricted and corresponding unrestricted controls. Specifically, plasma 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","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","NUM_GROUPS":"2","TOTAL_SUBJECTS":"10","NUM_MALES":"10","STUDY_COMMENTS":"Study 2 for datatrack 1972"},

"SUBJECT":{"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"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"-",
"Sample ID":"AR121_1-2",
"Factors":{"Diet":"Control (normal protein diet) D12450B"},
"Additional sample data":{"RAW_FILE_NAME":"C120180705_AR121_1-2_1.raw"}
},
{
"Subject ID":"-",
"Sample ID":"AR122_1-3",
"Factors":{"Diet":"Control (normal protein diet) D12450B"},
"Additional sample data":{"RAW_FILE_NAME":"C120180705_AR122_1-3_1.raw"}
},
{
"Subject ID":"-",
"Sample ID":"AR123_2-1",
"Factors":{"Diet":"Control (normal protein diet) D12450B"},
"Additional sample data":{"RAW_FILE_NAME":"C120180705_AR123_2-1_1.raw"}
},
{
"Subject ID":"-",
"Sample ID":"AR124_2-2",
"Factors":{"Diet":"Control (normal protein diet) D12450B"},
"Additional sample data":{"RAW_FILE_NAME":"C120180705_AR124_2-2_1.raw"}
},
{
"Subject ID":"-",
"Sample ID":"AR125_2-3",
"Factors":{"Diet":"Control (normal protein diet) D12450B"},
"Additional sample data":{"RAW_FILE_NAME":"C120180705_AR125_2-3_1.raw"}
},
{
"Subject ID":"-",
"Sample ID":"AR126_3-2",
"Factors":{"Diet":"Reduced protein diet D10062201"},
"Additional sample data":{"RAW_FILE_NAME":"C120180705_AR126_3-2_1.raw"}
},
{
"Subject ID":"-",
"Sample ID":"AR127_3-3",
"Factors":{"Diet":"Reduced protein diet D10062201"},
"Additional sample data":{"RAW_FILE_NAME":"C120180705_AR127_3-3_1.raw"}
},
{
"Subject ID":"-",
"Sample ID":"AR128_4-1",
"Factors":{"Diet":"Reduced protein diet D10062201"},
"Additional sample data":{"RAW_FILE_NAME":"C120180705_AR128_4-1_1.raw"}
},
{
"Subject ID":"-",
"Sample ID":"AR129_4-2",
"Factors":{"Diet":"Reduced protein diet D10062201"},
"Additional sample data":{"RAW_FILE_NAME":"C120180705_AR129_4-2_1.raw"}
},
{
"Subject ID":"-",
"Sample ID":"AR130_4-3",
"Factors":{"Diet":"Reduced protein diet D10062201"},
"Additional sample data":{"RAW_FILE_NAME":"C120180705_AR130_4-3_1.raw"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"Mice were fasted overnight and then re-fed for 5 to 6 hours before blood was collected from the hepatic portal vein.","SAMPLE_TYPE":"Blood (plasma)","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 (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 sample collections and being humanely euthanised for tissue collection."},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"Plasma (25 µL) was extracted by addition of 200 µL of 1:1 acetonitrile:MeOH v/v with 1 µM CHAPS, CAPS, PIPES and TRIS as internal standards at 0°C. Samples were then mixed on a vortex mixer for 30 minutes at 4°C after which they were centrifuged (20,000 rcf, 4℃, 15 min) and the supernatant then transferred to a mass spectrometry vial for LC-MS analysis.","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.","CHROMATOGRAPHY_TYPE":"HILIC","INSTRUMENT_NAME":"Thermo Dionex Ultimate 3000 RS","COLUMN_NAME":"SeQuant ZIC- pHILIC (150 x 4.6 mm, 5uM)"},

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

"MS":{"INSTRUMENT_NAME":"Thermo Q Exactive Orbitrap","INSTRUMENT_TYPE":"Orbitrap","MS_TYPE":"ESI","ION_MODE":"UNSPECIFIED","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).","MS_RESULTS_FILE":"ST001347_AN002241_Results.txt UNITS:Peak Area Has m/z:Neutral masses Has RT:Yes RT units:Minutes"}

}