Summary of Study ST000340
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 PR000272. The data can be accessed directly via it's Project DOI: 10.21228/M8MS4X This work is supported by NIH grant, U2C- DK119886.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
| Study ID | ST000340 |
| Study Title | Metformin effects on liver and kidney tissue |
| Study Summary | This experiment aimed to discover the effects of metformin on mouse liver and kidney tissue. The effects were seen by comparing the liver of the metformin group to the liver of a control group of mice treated given saline solution. |
| 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 | 2014-10-14 |
| Num Groups | 4 |
| Total Subjects | 20 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | d |
| 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: | PR000272 |
| Project DOI: | doi: 10.21228/M8MS4X |
| Project Title: | Metformin effects on liver and kidney tissue |
| Project Summary: | This experiment aimed to discover the effects of metformin on mouse liver and kidney tissue. The effects were seen by comparing the liver of the metformin group to the liver of a control group of mice treated given saline solution. |
| 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: | NIH U24DK097154 |
Subject:
| Subject ID: | SU000360 |
| Subject Type: | Animal |
| Subject Species: | Mus musculus |
| Taxonomy ID: | 10090 |
| Species Group: | Mammal |
Factors:
Subject type: Animal; Subject species: Mus musculus (Factor headings shown in green)
| mb_sample_id | local_sample_id | Treatment | Organ |
|---|---|---|---|
| SA015151 | Inj04_Kid Met_1 | Metformin | Kidney |
| SA015152 | Inj19_Kid Met_4 | Metformin | Kidney |
| SA015153 | Inj02_Kid Met_5 | Metformin | Kidney |
| SA015154 | Inj09_Kid Met_3 | Metformin | Kidney |
| SA015155 | Inj07_Kid Met_2 | Metformin | Kidney |
| SA015156 | Inj06_Liv Met_2 | Metformin | Liver |
| SA015157 | Inj13_Liv Met_3 | Metformin | Liver |
| SA015158 | Inj11_Liv Met_5 | Metformin | Liver |
| SA015159 | Inj20_Liv Met_4 | Metformin | Liver |
| SA015160 | Inj18_Liv Met_1 | Metformin | Liver |
| SA015161 | Inj01_Kid Sal_1 | Saline | Kidney |
| SA015162 | Inj03_Kid Sal_5 | Saline | Kidney |
| SA015163 | Inj12_Kid Sal_2 | Saline | Kidney |
| SA015164 | Inj15_Kid Sal_4 | Saline | Kidney |
| SA015165 | Inj17_Kid Sal_3 | Saline | Kidney |
| SA015166 | Inj14_Liv Sal_5 | Saline | Liver |
| SA015167 | Inj08_Liv Sal_4 | Saline | Liver |
| SA015168 | Inj10_Liv Sal_1 | Saline | Liver |
| SA015169 | Inj16_Liv Sal_2 | Saline | Liver |
| SA015170 | Inj05_Liv Sal_3 | Saline | Liver |
| Showing results 1 to 20 of 20 |
Collection:
| Collection ID: | CO000354 |
| Collection Summary: | Liver tissues were isolated and frozen down in liquid nitrogen. |
| Collection Protocol Filename: | SookWahYee_StudyDesign_5.13.14.pdf |
| Sample Type: | Liver and Kidney tissue |
Treatment:
| Treatment ID: | TR000374 |
| Treatment Summary: | 5 mice were treated with biguanide (metformin) and 5 mice were treated with saline. Liver tissues were obtained 7 days after treatment. |
| Treatment Protocol Filename: | SookWahYee_StudyDesign_5.13.14.pdf |
Sample Preparation:
| Sampleprep ID: | SP000367 |
| Sampleprep Summary: | 1. Weigh 4mg tissue sample in to a 2mL Eppendorf tube. 2. Add 1mL 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 in the order listed. 3. Vortex samples for 10 seconds, then 5 minutes on 4°C shaker. 4. Centrifuge the samples for 2 minutes at 14,000 rcf. Aliquot 500μL supernatant for analysis, and 500μL for a backup. Store backup aliquots in the -20°C freezer. 5. Evaporate one 500μl analysis aliquot in the Labconco Centrivap cold trap concentrator to complete dryness (typically overnight). 6. The dried aliquot is then re-suspended with 500l 50% acetonitrile (degassed as given) 7. Centrifuge for 2 minutes at 14,000 rcf using the centrifuge Eppendorf 5415. 8. Remove supernatant to a new Eppendorf tube. 9. Evaporate the supernatant to dryness in the the Labconco Centrivap cold trap concentrator. 10. Submit to derivatization. |
| Sampleprep Protocol Filename: | SOP Extraction of Liver Tissue Samples.pdf |
Combined analysis:
| Analysis ID | AN000552 |
|---|---|
| Analysis type | MS |
| Chromatography type | HILIC |
| Chromatography system | Unspecified |
| Column | Waters Acquity BEH Amide (150 x 2.1mm,1.7um) |
| MS Type | ESI |
| MS instrument type | QTOF |
| MS instrument name | Agilent 6530 QTOF |
| Ion Mode | POSITIVE |
| Units | Peak height |
Chromatography:
| Chromatography ID: | CH000389 |
| Methods Filename: | Data_Dictionary_Fiehn_laboratory_HILIC_QTOF_MS.pdf |
| Instrument Name: | Unspecified |
| Column Name: | Waters Acquity BEH Amide (150 x 2.1mm,1.7um) |
| Column Pressure: | 200-700 bar |
| Column Temperature: | 45 C |
| Flow Gradient: | 100% B to 30% B |
| Flow Rate: | 0.4 mL/min |
| Injection Temperature: | 4 C |
| Internal Standard: | See data dictionary |
| Sample Injection: | 3 μL |
| Analytical Time: | 14 min |
| Capillary Voltage: | 4500 |
| Time Program: | 16.75 min |
| Weak Wash Solvent Name: | 1:1 ACN:H2O |
| Weak Wash Volume: | 5 seconds |
| Target Sample Temperature: | Autosampler temp 4 C |
| Randomization Order: | Excel |
| Chromatography Type: | HILIC |
MS:
| MS ID: | MS000488 |
| Analysis ID: | AN000552 |
| Instrument Name: | Agilent 6530 QTOF |
| Instrument Type: | QTOF |
| MS Type: | ESI |
| 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 |
| Dataformat: | .d |
| 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 |
