Summary of Study ST000321
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 PR000260. The data can be accessed directly via it's Project DOI: 10.21228/M85S3H This work is supported by NIH grant, U2C- DK119886.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
| Study ID | ST000321 |
| Study Title | Effects of LGG on current drinkers gut metabolism |
| Study Summary | This experiment tests the effects of alcoholism by examining the primary metabolites obtained from mouse stool. Stool was collected from 4 groups of mice with varying treatments. One group was not humanized, another was humanized from a healthy human, a third was humanized from a current drinker, and the final group was humanized from a current drinker but also given a treatment of LGG. Humanizations were done to create a model of human gut activity in the mice. |
| Institute | University of California, Davis |
| Department | Genome and Biomedical Sciences Facility |
| Laboratory | WCMC Metabolomics Core |
| Last Name | Fiehn |
| First Name | Oliver |
| Address | 1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616 |
| ofiehn@ucdavis.edu | |
| Phone | (530) 754-8258 |
| Submit Date | 2014-12-22 |
| Num Groups | 8 |
| Total Subjects | 56 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | d |
| Analysis Type Detail | LC-MS |
| Release Date | 2016-01-27 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR000260 |
| Project DOI: | doi: 10.21228/M85S3H |
| Project Title: | Effects of LGG on current drinkers gut metabolism |
| Project Summary: | This experiment tests the effects of alcoholism by examining the primary metabolites obtained from mouse stool. Stool was collected from 4 groups of mice with varying treatments. One group was not humanized, another was humanized from a healthy human, a third was humanized from a current drinker, and the final group was humanized from a current drinker but also given a treatment of LGG. Humanizations were done to create a model of human gut activity in the mice. |
| Institute: | University of California, Davis |
| Department: | Genome and Biomedical Sciences Facility |
| Laboratory: | WCMC Metabolomics Core |
| Last Name: | Fiehn |
| First Name: | Oliver |
| Address: | 1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616 |
| Email: | ofiehn@ucdavis.edu |
| Phone: | (530) 754-8258 |
| Funding Source: | U24DK097154 |
Subject:
| Subject ID: | SU000341 |
| Subject Type: | Animal |
| Subject Species: | Mus musculus |
| Taxonomy ID: | 10090 |
| Species Group: | Mammals |
Factors:
Subject type: Animal; Subject species: Mus musculus (Factor headings shown in green)
| mb_sample_id | local_sample_id | Treatment |
|---|---|---|
| SA014514 | ACI7-CC | Alcoholic cirrhosis infusion |
| SA014515 | ACI9-CC | Alcoholic cirrhosis infusion |
| SA014516 | ACI6-CC | Alcoholic cirrhosis infusion |
| SA014517 | ACI1-CC | Alcoholic cirrhosis infusion |
| SA014518 | ACI8-CC | Alcoholic cirrhosis infusion |
| SA014519 | ACI5-CC | Alcoholic cirrhosis infusion |
| SA014520 | ACI3-CC | Alcoholic cirrhosis infusion |
| SA014521 | ACI4-CC | Alcoholic cirrhosis infusion |
| SA014522 | ACI2-CC | Alcoholic cirrhosis infusion |
| SA014523 | CR1-CC | Germ Free Control |
| SA014524 | CR2-CC | Germ Free Control |
| SA014525 | CR4-CC | Germ Free Control |
| SA014526 | CR3-CC | Germ Free Control |
| SA014527 | LG9-CC | LGG Treated |
| SA014528 | LG8-CC | LGG Treated |
| SA014529 | LG6-CC | LGG Treated |
| SA014530 | LG7-CC | LGG Treated |
| SA014531 | LG1-CC | LGG Treated |
| SA014532 | LG2-CC | LGG Treated |
| SA014533 | LG3-CC | LGG Treated |
| SA014534 | LG5-CC | LGG Treated |
| SA014535 | LG4-CC | LGG Treated |
| SA014536 | 6 HIGF-6 | Normal Human Infusion |
| SA014537 | 5 HIGF-5 | Normal Human Infusion |
| SA014538 | 1 HIGF-1 | Normal Human Infusion |
| SA014539 | 2 HIGF-2 | Normal Human Infusion |
| SA014540 | 3 HIGF-3 | Normal Human Infusion |
| SA014541 | 4 HIGF-4 | Normal Human Infusion |
| Showing results 1 to 28 of 28 |
Collection:
| Collection ID: | CO000335 |
| Collection Summary: | Cecal contents |
| Collection Protocol Filename: | StudyDesign-AvinashSrivastava-82514.pdf |
| Sample Type: | Stool |
Treatment:
| Treatment ID: | TR000355 |
| Treatment Summary: | 4 treatments: 4 mice who are germ-free (CR1-CC through CR 4 CC) 6 mice who have been humanized with stool from a healthy human (harvested at 30 days) (HI1-LC through HI6-LC) 9 mice who have been humanized with stool from a current drinker(harvested at 30 days) (ACL1-CC through ACL-9-CC) and 9 mice who have been humanized with stool from a current drinker and then supplemented with LGG (harvested at 30 days with 15 days of LGG, LG1-CC through LG9-CC) |
| Treatment Protocol Filename: | StudyDesign_JasBajaj_8414.pdf |
Sample Preparation:
| Sampleprep ID: | SP000349 |
| Sampleprep Summary: | Preparation of extraction mix and material before experiment: 1. Switch on bath to pre-cool at –20°C (2°C validity temperature range) 2. Check pH of acetonitrile and isopropanol (pH7) using wetted pH paper 3. Make the extraction solution by missing acetonitrile, isopropanol and water in proportions 3 : 3 : 2 4. Rinse the extraction solution for 5 min with nitrogen. Make sure that the nitrogen line was flushed out of air before using it for degassing the extraction solvent solution Sample Preparation 1. Weigh 50 mg tissue sample in to a 25 ml conical polypropylene centrifuge tube. 2. Add 2.5mL extraction solvent to the tissue sample and homogenize for 45 seconds ensuring that sample resembles a powder. In between samples, clean the homogenizer in solutions of methanol, acetone, water, and the extraction solvent. 3. Centrifuge the samples at 2500 rpm. for 5 minutes. Aliquot 2 X 500µl supernatant, one for analysis and one for a backup sample. Store backup aliquot in the -20°C freezer. 4. Evaporate one 500µl aliquot of the sample in the Labconco Centrivap cold trap concentrator to complete dryness 5. The dried aliquot is then re-suspended with 500l 50% acetonitrile (degassed as given) 6. Centrifuge for 2 min at 14000 rcf using the centrifuge Eppendorf 5415. 7. Remove supernatant to a new Eppendorff tube. 8. Evaporate the supernatant to dryness in the the Labconco Centrivap cold trap concentrator. 9. Submit to derivatization. |
| Sampleprep Protocol Filename: | SOP_Extraction_of_Mammalian_Tissue_Samples.pdf |
Combined analysis:
| Analysis ID | AN000510 | AN000511 |
|---|---|---|
| Analysis type | MS | MS |
| Chromatography type | Reversed phase | Reversed phase |
| Chromatography system | Unspecified | Unspecified |
| Column | Waters Acquity CSH C18 (100 x 2.1mm,1.7um) | Waters Acquity CSH C18 (100 x 2.1mm,1.7um) |
| MS Type | ESI | ESI |
| MS instrument type | QTOF | QTOF |
| MS instrument name | Agilent 6530 QTOF | Agilent 6550 QTOF |
| Ion Mode | POSITIVE | NEGATIVE |
| Units | Peak height | Peak height |
Chromatography:
| Chromatography ID: | CH000359 |
| Chromatography Summary: | UPLC |
| Methods Filename: | Data_Dictionary_Fiehn_laboratory_CSH_QTOF_lipidomics_05-29-2014.pdf |
| Instrument Name: | Unspecified |
| Column Name: | Waters Acquity CSH C18 (100 x 2.1mm,1.7um) |
| Column Pressure: | 450-850 bar |
| Column Temperature: | 65 C |
| Flow Gradient: | 15% B to 99% B |
| Flow Rate: | 0.6 mL/min |
| Internal Standard: | See data dictionary |
| Retention Time: | See data dictionary |
| Sample Injection: | 1.67 uL |
| Solvent A: | 60% acetonitrile/40% water; 10mM formic acid; 10mM ammonium formate |
| Solvent B: | 90% isopropanol/10% acetonitrile; 10mM formic acid; 10mM ammonium formate |
| Analytical Time: | 13 min |
| Capillary Voltage: | 3500 |
| Time Program: | 15 min |
| Weak Wash Solvent Name: | Isopropanol |
| Weak Wash Volume: | 5 seconds |
| Strong Wash Solvent Name: | Isopropanol |
| Target Sample Temperature: | Autosampler temp 4 C |
| Randomization Order: | Excel |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS000446 |
| Analysis ID: | AN000510 |
| Instrument Name: | Agilent 6530 QTOF |
| Instrument Type: | QTOF |
| MS Type: | ESI |
| MS Comments: | Lipidomics runs are MS1 data; Identifications made from pooled MS/MS runs |
| Ion Mode: | POSITIVE |
| Capillary Voltage: | 3500 |
| Collision Gas: | Nitrogen |
| Dry Gas Flow: | 8 l/min |
| Dry Gas Temp: | 325 |
| Fragment Voltage: | 120 |
| Fragmentation Method: | Auto MS/MS |
| Ion Source Temperature: | 325 |
| Ion Spray Voltage: | 1000 |
| Ionization: | Pos |
| Precursor Type: | Intact Molecule |
| Reagent Gas: | Nitrogen |
| Source Temperature: | 325 C |
| Desolvation Gas Flow: | 11 l/min |
| Desolvation Temperature: | 350 C |
| Nebulizer: | 35 psig |
| Octpole Voltage: | 750 |
| Resolution Setting: | Extended Dynamic Range |
| Scan Range Moverz: | 60-1700 Da |
| Scanning Cycle: | 2 Hz |
| Scanning Range: | 60-1700 Da |
| Skimmer Voltage: | 65 |
| MS ID: | MS000447 |
| Analysis ID: | AN000511 |
| Instrument Name: | Agilent 6550 QTOF |
| Instrument Type: | QTOF |
| MS Type: | ESI |
| MS Comments: | Lipidomics runs are MS1 data; Identifications made from pooled MS/MS runs |
| Ion Mode: | NEGATIVE |
| Capillary Voltage: | 3500 |
| Collision Gas: | Nitrogen |
| Dry Gas Flow: | 8 l/min |
| Dry Gas Temp: | 325 |
| Fragment Voltage: | 120 |
| Fragmentation Method: | Auto MS/MS |
| Ion Source Temperature: | 325 |
| Ion Spray Voltage: | 1000 |
| Ionization: | Pos |
| Precursor Type: | Intact Molecule |
| Reagent Gas: | Nitrogen |
| Source Temperature: | 325 C |
| Desolvation Gas Flow: | 11 l/min |
| Desolvation Temperature: | 350 C |
| Nebulizer: | 35 psig |
| Octpole Voltage: | 750 |
| Resolution Setting: | Extended Dynamic Range |
| Scan Range Moverz: | 60-1700 Da |
| Scanning Cycle: | 2 Hz |
| Scanning Range: | 60-1700 Da |
| Skimmer Voltage: | 65 |
