{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST000254","ANALYSIS_ID":"AN000402","VERSION":"1","CREATED_ON":"02-08-2024"},

"PROJECT":{"PROJECT_TITLE":"The role of microbial metabolites in experimental liver disease","PROJECT_TYPE":"Targeted Metabolomics","PROJECT_SUMMARY":"Liver fibrosis is the result of chronic liver damage from various etiologies including toxins, alcohol abuse, obesity, or viral hepatitis. Chronic liver disease may progress to cirrhosis, an end stage organ disease, and liver cancer. Patients with chronic liver disease show intestinal bacterial overgrowth and dysbiosis. They also demonstrate increased intestinal permeability, and disease severity correlates with systemic levels of bacterial products. Although experimental liver fibrosis is dependent on gut derived bacterial products, the exact contribution of the commensal microflora to chronic liver disease in unknown. Since the interaction of bacterial products with the innate immune system can also confer protection to the host, we subjected germfree mice to experimental models of liver fibrosis. Results from our laboratory demonstrate that germfree mice show exacerbated liver fibrosis as compared to conventional mice. Our previous studies also have indicated that a bacterial metabolite of tryptophan, Indole-3-propionic Acid (IPA), is absent in germ free mice. In this study we are investigating the role of IPA in acute and chronic models of liver fibrosis.","INSTITUTE":"University of California, San Diego","LAST_NAME":"Schnabl","FIRST_NAME":"Bernd","ADDRESS":"9500 Gilman Drive, MC0063 La Jolla, CA 92093","EMAIL":"beschnabl@ucsd.edu","PHONE":"858-822-5311","DOI":"http://dx.doi.org/10.21228/M8RW2F"},

"STUDY":{"STUDY_TITLE":"The role of microbial metabolites in experimental liver disease","STUDY_TYPE":"Targeted Metabolomic Analysis of plasma samples","STUDY_SUMMARY":"Aim 1: Our experimental approach is to understand the effect of drinking water supplemented bacterial metabolite, Indole-3-propionic Acid (IPA), in liver disease in an acute alcohol model. Aim 2: Determine the levels of IPA in plasma of conventional mice in a chronic alcohol model. Aim 3: Determine the levels of IPA in plasma of conventional WT (C57BL/6) and mutant SL (sublytic, which is a mouse with a point mutation in ATP4a) mice.","INSTITUTE":"University of North Carolina","DEPARTMENT":"Discovery Science Technology","LABORATORY":"Sumner Lab","LAST_NAME":"Sumner","FIRST_NAME":"Susan","ADDRESS":"Eastern Regional Comprehensive Metabolomics Resource Core, UNC Nutrition Research Institute, 500 Laureate Way, Kannapolis, NC, 28081","EMAIL":"susan_sumner @unc.edu","PHONE":"704-250-5066","SUBMIT_DATE":"2015-09-29"},

"SUBJECT":{"SUBJECT_TYPE":"Animal","SUBJECT_SPECIES":"Mus musculus","TAXONOMY_ID":"10090","GENOTYPE_STRAIN":"C57BL/6","SPECIES_GROUP":"Mammal"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"-",
"Sample ID":"P7",
"Factors":{"Groups":"Acute Alcohol Model","Treatment":"0 mM IPA","Strain":"WT"}
},
{
"Subject ID":"-",
"Sample ID":"P8",
"Factors":{"Groups":"Acute Alcohol Model","Treatment":"0 mM IPA","Strain":"WT"}
},
{
"Subject ID":"-",
"Sample ID":"P13",
"Factors":{"Groups":"Acute Alcohol Model","Treatment":"10 mM IPA","Strain":"WT"}
},
{
"Subject ID":"-",
"Sample ID":"P14",
"Factors":{"Groups":"Acute Alcohol Model","Treatment":"10 mM IPA","Strain":"WT"}
},
{
"Subject ID":"-",
"Sample ID":"P15",
"Factors":{"Groups":"Acute Alcohol Model","Treatment":"10 mM IPA","Strain":"WT"}
},
{
"Subject ID":"-",
"Sample ID":"P10",
"Factors":{"Groups":"Acute Alcohol Model","Treatment":"1 mM IPA","Strain":"WT"}
},
{
"Subject ID":"-",
"Sample ID":"P11",
"Factors":{"Groups":"Acute Alcohol Model","Treatment":"1 mM IPA","Strain":"WT"}
},
{
"Subject ID":"-",
"Sample ID":"P12",
"Factors":{"Groups":"Acute Alcohol Model","Treatment":"1 mM IPA","Strain":"WT"}
},
{
"Subject ID":"-",
"Sample ID":"P9",
"Factors":{"Groups":"Acute Alcohol Model","Treatment":"1 mM IPA","Strain":"WT"}
},
{
"Subject ID":"-",
"Sample ID":"STD10",
"Factors":{"Groups":"Calibration Standard 10","Treatment":"2000 ng/ml of IPA","Strain":"N/A"}
},
{
"Subject ID":"-",
"Sample ID":"STD11",
"Factors":{"Groups":"Calibration Standard 11","Treatment":"2500 ng/ml of IPA","Strain":"N/A"}
},
{
"Subject ID":"-",
"Sample ID":"STD12",
"Factors":{"Groups":"Calibration Standard 12","Treatment":"3000 ng/ml of IPA","Strain":"N/A"}
},
{
"Subject ID":"-",
"Sample ID":"STD1",
"Factors":{"Groups":"Calibration Standard 1","Treatment":"10 ng/ml of IPA","Strain":"N/A"}
},
{
"Subject ID":"-",
"Sample ID":"STD2",
"Factors":{"Groups":"Calibration Standard 2","Treatment":"20 ng/ml of IPA","Strain":"N/A"}
},
{
"Subject ID":"-",
"Sample ID":"STD3",
"Factors":{"Groups":"Calibration Standard 3","Treatment":"40 ng/ml of IPA","Strain":"N/A"}
},
{
"Subject ID":"-",
"Sample ID":"STD4",
"Factors":{"Groups":"Calibration Standard 4","Treatment":"80 ng/ml of IPA","Strain":"N/A"}
},
{
"Subject ID":"-",
"Sample ID":"STD5",
"Factors":{"Groups":"Calibration Standard 5","Treatment":"160 ng/ml of IPA","Strain":"N/A"}
},
{
"Subject ID":"-",
"Sample ID":"STD6",
"Factors":{"Groups":"Calibration Standard 6","Treatment":"320 ng/ml of IPA","Strain":"N/A"}
},
{
"Subject ID":"-",
"Sample ID":"STD7",
"Factors":{"Groups":"Calibration Standard 7","Treatment":"650 ng/ml of IPA","Strain":"N/A"}
},
{
"Subject ID":"-",
"Sample ID":"STD8",
"Factors":{"Groups":"Calibration Standard 8","Treatment":"1000 ng/ml of IPA","Strain":"N/A"}
},
{
"Subject ID":"-",
"Sample ID":"STD9",
"Factors":{"Groups":"Calibration Standard 9","Treatment":"1500 ng/ml of IPA","Strain":"N/A"}
},
{
"Subject ID":"-",
"Sample ID":"P28",
"Factors":{"Groups":"Chronic Alcohol Model","Treatment":"No IPA","Strain":"SL"}
},
{
"Subject ID":"-",
"Sample ID":"P29",
"Factors":{"Groups":"Chronic Alcohol Model","Treatment":"No IPA","Strain":"SL"}
},
{
"Subject ID":"-",
"Sample ID":"P30",
"Factors":{"Groups":"Chronic Alcohol Model","Treatment":"No IPA","Strain":"SL"}
},
{
"Subject ID":"-",
"Sample ID":"P31",
"Factors":{"Groups":"Chronic Alcohol Model","Treatment":"No IPA","Strain":"SL"}
},
{
"Subject ID":"-",
"Sample ID":"P20",
"Factors":{"Groups":"Chronic Alcohol Model","Treatment":"No IPA","Strain":"WT"}
},
{
"Subject ID":"-",
"Sample ID":"P21",
"Factors":{"Groups":"Chronic Alcohol Model","Treatment":"No IPA","Strain":"WT"}
},
{
"Subject ID":"-",
"Sample ID":"P22",
"Factors":{"Groups":"Chronic Alcohol Model","Treatment":"No IPA","Strain":"WT"}
},
{
"Subject ID":"-",
"Sample ID":"P23",
"Factors":{"Groups":"Chronic Alcohol Model","Treatment":"No IPA","Strain":"WT"}
},
{
"Subject ID":"-",
"Sample ID":"P24",
"Factors":{"Groups":"Chronic Alcohol Model","Treatment":"No IPA","Strain":"WT"}
},
{
"Subject ID":"-",
"Sample ID":"P25",
"Factors":{"Groups":"Chronic Alcohol Model","Treatment":"No IPA","Strain":"WT"}
},
{
"Subject ID":"-",
"Sample ID":"P26",
"Factors":{"Groups":"Chronic Alcohol Model","Treatment":"No IPA","Strain":"WT"}
},
{
"Subject ID":"-",
"Sample ID":"P27",
"Factors":{"Groups":"Chronic Alcohol Model","Treatment":"No IPA","Strain":"WT"}
},
{
"Subject ID":"-",
"Sample ID":"P1",
"Factors":{"Groups":"Control","Treatment":"0 mM IPA","Strain":"WT"}
},
{
"Subject ID":"-",
"Sample ID":"P2",
"Factors":{"Groups":"Control","Treatment":"0 mM IPA","Strain":"WT"}
},
{
"Subject ID":"-",
"Sample ID":"P5",
"Factors":{"Groups":"Control","Treatment":"10 mM IPA","Strain":"WT"}
},
{
"Subject ID":"-",
"Sample ID":"P6",
"Factors":{"Groups":"Control","Treatment":"10 mM IPA","Strain":"WT"}
},
{
"Subject ID":"-",
"Sample ID":"P3",
"Factors":{"Groups":"Control","Treatment":"1 mM IPA","Strain":"WT"}
},
{
"Subject ID":"-",
"Sample ID":"P4",
"Factors":{"Groups":"Control","Treatment":"1 mM IPA","Strain":"WT"}
},
{
"Subject ID":"-",
"Sample ID":"P16",
"Factors":{"Groups":"Control","Treatment":"No IPA","Strain":"WT"}
},
{
"Subject ID":"-",
"Sample ID":"P17",
"Factors":{"Groups":"Control","Treatment":"No IPA","Strain":"WT"}
},
{
"Subject ID":"-",
"Sample ID":"P18",
"Factors":{"Groups":"Control","Treatment":"No IPA","Strain":"WT"}
},
{
"Subject ID":"-",
"Sample ID":"P19",
"Factors":{"Groups":"Control","Treatment":"No IPA","Strain":"WT"}
},
{
"Subject ID":"-",
"Sample ID":"QC1",
"Factors":{"Groups":"Quality Control Sample 1","Treatment":"30 ng/ml of IPA","Strain":"N/A"}
},
{
"Subject ID":"-",
"Sample ID":"QC2",
"Factors":{"Groups":"Quality Control Sample 2","Treatment":"200 ng/ml of IPA","Strain":"N/A"}
},
{
"Subject ID":"-",
"Sample ID":"QC3",
"Factors":{"Groups":"Quality Control Sample 3","Treatment":"600 ng/ml of IPA","Strain":"N/A"}
},
{
"Subject ID":"-",
"Sample ID":"QC4",
"Factors":{"Groups":"Quality Control Sample 4","Treatment":"1800 ng/ml of IPA","Strain":"N/A"}
},
{
"Subject ID":"-",
"Sample ID":"QC5",
"Factors":{"Groups":"Quality Control Sample 5","Treatment":"2400 ng/ml of IPA","Strain":"N/A"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"-","SAMPLE_TYPE":"Blood"},

"TREATMENT":{"TREATMENT_SUMMARY":"Control vs IPA Supplemented Wild Type and SL Mice","TREATMENT":"Indole-3-propionic Acid (IPA) Supplemention","TREATMENT_COMPOUND":"Indole-3-propionic Acid (IPA)","TREATMENT_ROUTE":"Drinking Water","TREATMENT_DOSE":"0, 1, and 10 mM IPA"},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"Aliquots of plasma samples (20 µL) were transferred into pre-labeled 2.0 mL low-bind Eppendorf tubes for experimental samples.  For all samples 100 µL Protein Precipitation Buffer with internal standard [2.5 ng/ml of 2-methyl-4-chlorophenyl-acetic acid (MCPA) in methanol] was added to each tube and were vortexed for 2 min at 5000 rpm.  The samples were centrifuged at 16,000 rcf for 4 min. A 90 µL of the supernatant wastransferred into pre-labeled auto-sampler vials and diluted by adding 90 µL of water with 10% Formic Acid. Samples were then mixed on a multiple tube vortexer for 5 min at 5000 rpm.  10 µL of samples were injected onto API-4000 Q-trap.","PROCESSING_STORAGE_CONDITIONS":"4°C","EXTRACT_STORAGE":"-80C","SAMPLE_RESUSPENSION":"Methanol, H2O, formic acid","SAMPLE_SPIKING":"2-methyl-4-chlorophenyl-acetic acid (MCPA)"},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_SUMMARY":"Reversed-Phase Gradient Seperation","METHODS_ID":"RTI-RCMRC-IPA-Analysis","METHODS_FILENAME":"RTI-RCMRC-IPA-Analysis","INSTRUMENT_NAME":"Waters Acquity","COLUMN_NAME":"Waters Acquity BEH C18 (50 x 2.1mm,1.7um)","COLUMN_PRESSURE":"6000-10000","COLUMN_TEMPERATURE":"50 C","FLOW_GRADIENT":"Time(min) Flow Rate  %A  %B  Curve ;Initial  0.600   99.0  1.0  6;0.75   0.600   99.0  1.0  6 ;2.75   0.600   1.0  99.0 6 ;3.00   0.600   1.0  99.0  6 ;3.10   0.600   99.0  1.0  6 ;3.50   0.600   99.0  1.0  6;","FLOW_RATE":"0.6 ml/min","INJECTION_TEMPERATURE":"8 C","INTERNAL_STANDARD":"2-methyl-4-chlorophenyl-acetic acid (MCPA)","SOLVENT_A":"95% water/5% acetonitrile; 0.15% acetic acid","SOLVENT_B":"95% acetonitrile/5% water; 0.15% acetic acid","ANALYTICAL_TIME":"3.5 mins","WEAK_WASH_SOLVENT_NAME":"95:5 Water:ACN with 0.15% Acetic Acid","WEAK_WASH_VOLUME":"600 uL","STRONG_WASH_SOLVENT_NAME":"95:5 ACN:Water with 0.15% Acetic Acid","STRONG_WASH_VOLUME":"600 uL","TARGET_SAMPLE_TEMPERATURE":"8 C","SAMPLE_LOOP_SIZE":"10 uL","SAMPLE_SYRINGE_SIZE":"100 uL","RANDOMIZATION_ORDER":"Yes","CHROMATOGRAPHY_TYPE":"Reversed phase"},

"ANALYSIS":{"LABORATORY_NAME":"RTI","ANALYSIS_TYPE":"MS","ACQUISITION_DATE":"42166","ACQUISITION_PARAMETERS_FILE":"RTI-RCMRC-IPA-Analysis","SOFTWARE_VERSION":"Analyst 1.6.2","OPERATOR_NAME":"Suraj Dhungana","PROCESSING_PARAMETERS_FILE":"RTI-RCMRC-IPA-Analysis","DETECTOR_TYPE":"TOF"},

"MS":{"INSTRUMENT_NAME":"ABI Sciex API 4000 QTrap","INSTRUMENT_TYPE":"Triple quadrupole","MS_TYPE":"ESI","ION_MODE":"NEGATIVE","COLLISION_ENERGY":"-20","COLLISION_GAS":"6","ION_SOURCE_TEMPERATURE":"450 C","ION_SPRAY_VOLTAGE":"-4500 volts"}

}