Summary of Study ST000254
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 PR000206. The data can be accessed directly via it's Project DOI: 10.21228/M8RW2F This work is supported by NIH grant, U2C- DK119886.
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| Study ID | ST000254 |
| 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 |
| susan_sumner @unc.edu | |
| Phone | 704-250-5066 |
| Submit Date | 2015-09-29 |
| Num Groups | 2 |
| Total Subjects | 31 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | wiff |
| Uploaded File Size | 8.6 M |
| Analysis Type Detail | LC-MS |
| Release Date | 2016-12-22 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR000206 |
| Project DOI: | doi: 10.21228/M8RW2F |
| 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 |
Subject:
| Subject ID: | SU000274 |
| Subject Type: | Animal |
| Subject Species: | Mus musculus |
| Taxonomy ID: | 10090 |
| Genotype Strain: | C57BL/6 |
| Species Group: | Mammal |
Factors:
Subject type: Animal; Subject species: Mus musculus (Factor headings shown in green)
| mb_sample_id | local_sample_id | Groups | Treatment | Strain |
|---|---|---|---|---|
| SA011574 | P7 | Acute Alcohol Model | 0 mM IPA | WT |
| SA011575 | P8 | Acute Alcohol Model | 0 mM IPA | WT |
| SA011580 | P15 | Acute Alcohol Model | 10 mM IPA | WT |
| SA011581 | P14 | Acute Alcohol Model | 10 mM IPA | WT |
| SA011582 | P13 | Acute Alcohol Model | 10 mM IPA | WT |
| SA011576 | P10 | Acute Alcohol Model | 1 mM IPA | WT |
| SA011577 | P11 | Acute Alcohol Model | 1 mM IPA | WT |
| SA011578 | P12 | Acute Alcohol Model | 1 mM IPA | WT |
| SA011579 | P9 | Acute Alcohol Model | 1 mM IPA | WT |
| SA011583 | STD10 | Calibration Standard 10 | 2000 ng/ml of IPA | N/A |
| SA011584 | STD11 | Calibration Standard 11 | 2500 ng/ml of IPA | N/A |
| SA011585 | STD12 | Calibration Standard 12 | 3000 ng/ml of IPA | N/A |
| SA011586 | STD1 | Calibration Standard 1 | 10 ng/ml of IPA | N/A |
| SA011587 | STD2 | Calibration Standard 2 | 20 ng/ml of IPA | N/A |
| SA011588 | STD3 | Calibration Standard 3 | 40 ng/ml of IPA | N/A |
| SA011589 | STD4 | Calibration Standard 4 | 80 ng/ml of IPA | N/A |
| SA011590 | STD5 | Calibration Standard 5 | 160 ng/ml of IPA | N/A |
| SA011591 | STD6 | Calibration Standard 6 | 320 ng/ml of IPA | N/A |
| SA011592 | STD7 | Calibration Standard 7 | 650 ng/ml of IPA | N/A |
| SA011593 | STD8 | Calibration Standard 8 | 1000 ng/ml of IPA | N/A |
| SA011594 | STD9 | Calibration Standard 9 | 1500 ng/ml of IPA | N/A |
| SA011595 | P28 | Chronic Alcohol Model | No IPA | SL |
| SA011596 | P29 | Chronic Alcohol Model | No IPA | SL |
| SA011597 | P30 | Chronic Alcohol Model | No IPA | SL |
| SA011598 | P31 | Chronic Alcohol Model | No IPA | SL |
| SA011599 | P27 | Chronic Alcohol Model | No IPA | WT |
| SA011600 | P24 | Chronic Alcohol Model | No IPA | WT |
| SA011601 | P20 | Chronic Alcohol Model | No IPA | WT |
| SA011602 | P26 | Chronic Alcohol Model | No IPA | WT |
| SA011603 | P22 | Chronic Alcohol Model | No IPA | WT |
| SA011604 | P21 | Chronic Alcohol Model | No IPA | WT |
| SA011605 | P25 | Chronic Alcohol Model | No IPA | WT |
| SA011606 | P23 | Chronic Alcohol Model | No IPA | WT |
| SA011607 | P2 | Control | 0 mM IPA | WT |
| SA011608 | P1 | Control | 0 mM IPA | WT |
| SA011611 | P6 | Control | 10 mM IPA | WT |
| SA011612 | P5 | Control | 10 mM IPA | WT |
| SA011609 | P4 | Control | 1 mM IPA | WT |
| SA011610 | P3 | Control | 1 mM IPA | WT |
| SA011613 | P16 | Control | No IPA | WT |
| SA011614 | P19 | Control | No IPA | WT |
| SA011615 | P18 | Control | No IPA | WT |
| SA011616 | P17 | Control | No IPA | WT |
| SA011617 | QC1 | Quality Control Sample 1 | 30 ng/ml of IPA | N/A |
| SA011618 | QC2 | Quality Control Sample 2 | 200 ng/ml of IPA | N/A |
| SA011619 | QC3 | Quality Control Sample 3 | 600 ng/ml of IPA | N/A |
| SA011620 | QC4 | Quality Control Sample 4 | 1800 ng/ml of IPA | N/A |
| SA011621 | QC5 | Quality Control Sample 5 | 2400 ng/ml of IPA | N/A |
| Showing results 1 to 48 of 48 |
Collection:
| Collection ID: | CO000266 |
| Collection Summary: | - |
| Sample Type: | Blood |
Treatment:
| Treatment ID: | TR000286 |
| 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 |
Sample Preparation:
| Sampleprep ID: | SP000280 |
| 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) |
Combined analysis:
| Analysis ID | AN000402 |
|---|---|
| Analysis type | MS |
| Chromatography type | Reversed phase |
| Chromatography system | Waters Acquity |
| Column | Waters Acquity BEH C18 (50 x 2.1mm,1.7um) |
| MS Type | ESI |
| MS instrument type | Triple quadrupole |
| MS instrument name | ABI Sciex API 4000 QTrap |
| Ion Mode | NEGATIVE |
| Units |
Chromatography:
| Chromatography ID: | CH000284 |
| 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 |
MS:
| MS ID: | MS000346 |
| Analysis ID: | AN000402 |
| 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 |
| Acquisition Parameters File: | RTI-RCMRC-IPA-Analysis |
| Processing Parameters File: | RTI-RCMRC-IPA-Analysis |
