Summary of Study ST001366
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 PR000934. The data can be accessed directly via it's Project DOI: 10.21228/M8ZH61 This work is supported by NIH grant, U2C- DK119886.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.
| Study ID | ST001366 |
| Study Title | Malnutrition and Liver Metabolomics |
| Study Summary | RP-UPLC-FTMS (+/- ion detection) were conducted on hippocampi from healthy (CON) and malnourished (MAL) mice, and MAL-BG (malnutrition plus E.coli/Bacteroidales exposure) mice. |
| Institute | University of British Columbia |
| Department | Microbiology and Immunology |
| Laboratory | B. Brett Finlay |
| Last Name | Bauer |
| First Name | Kylynda |
| Address | Michael Smith Laboratories, #301 – 2185 East Mall, University of British Columbia Vancouver, British Columbia Canada, V6T 1Z4 |
| kcbauer@msl.ubc.ca | |
| Phone | (604) 822-2210 |
| Submit Date | 2020-04-24 |
| Num Groups | 3 |
| Total Subjects | 15 |
| Num Females | 15 |
| Raw Data Available | Yes |
| Analysis Type Detail | LC-MS |
| Release Date | 2021-06-30 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR000934 |
| Project DOI: | doi: 10.21228/M8ZH61 |
| Project Title: | Malnutrition, Microbes, and Hippocampal Metabolomics |
| Project Summary: | Examining the role of malnutrition and gut microbes on CNS function using the MAL-BG murine model. RP-UPLC-FTMS was conducted on murine hippocampal tissue. |
| Institute: | University of British Columbia |
| Department: | Microbiology and Immunology |
| Laboratory: | Finlay |
| Last Name: | Bauer |
| First Name: | Kylynda |
| Address: | #301 – 2185 East Mall, University of British Columbia Vancouver, British Columbia Canada, V6T 1Z4 |
| Email: | kcbauer@msl.ubc.ca |
| Phone: | (604) 822-2210 |
| Contributors: | B. Brett Finlay |
Subject:
| Subject ID: | SU001440 |
| Subject Type: | Mammal |
| Subject Species: | Mus musculus |
| Taxonomy ID: | 10090 |
| Genotype Strain: | C57BL/6J |
| Age Or Age Range: | 7 weeks |
| Gender: | Female |
| Animal Animal Supplier: | Jackson Laboratories |
| Species Group: | Mammals |
Factors:
Subject type: Mammal; Subject species: Mus musculus (Factor headings shown in green)
| mb_sample_id | local_sample_id | Treatment | Diet | Bacterial Exposure |
|---|---|---|---|---|
| SA099362 | CON_1 | CON | Healthy | No |
| SA099363 | CON_2 | CON | Healthy | No |
| SA099364 | CON_5 | CON | Healthy | No |
| SA099365 | CON_3 | CON | Healthy | No |
| SA099366 | CON_4 | CON | Healthy | No |
| SA099367 | MALBG_3 | MAL-BG | Malnourished | Yes |
| SA099368 | MALBG_1 | MAL-BG | Malnourished | Yes |
| SA099369 | MALBG_2 | MAL-BG | Malnourished | Yes |
| SA099370 | MALBG_5 | MAL-BG | Malnourished | Yes |
| SA099371 | MALBG_4 | MAL-BG | Malnourished | Yes |
| SA099372 | MAL_3 | MAL | Malnourished | No |
| SA099373 | MAL_1 | MAL | Malnourished | No |
| SA099374 | MAL_2 | MAL | Malnourished | No |
| SA099375 | MAL_4 | MAL | Malnourished | No |
| SA099376 | MAL_5 | MAL | Malnourished | No |
| Showing results 1 to 15 of 15 |
Collection:
| Collection ID: | CO001435 |
| Collection Summary: | Following sacrifice, murine liver lobes were isolated and stored at -70/80 C prior to untargeted metabolomics. |
| Sample Type: | Hippocampus |
Treatment:
| Treatment ID: | TR001455 |
| Treatment Summary: | CON = control mice on healthy diet, MAL = mice placed on a protein/fat deficient diet (malnourished), MAL-BG = MAL mice plus iterative E.coli/Bacteroidales exposure |
Sample Preparation:
| Sampleprep ID: | SP001448 |
| Sampleprep Summary: | Methods reported in methodology .zip folder / Metabolomics were completed by TMIC (The Metabolomics Innovation Centre). Each mouse hippocampal sample in an Eppendorf tube was mixed with water, 5 μL per mg of the tissue, and two 4-mm metal balls were added. The tissue was homogenized on a MM 400 mill mixer at a vibrating frequency of 30 Hz for 1 min twice. After 5-s spin-down, a mixture of methanol-chloroform (4:1) was added, at 25 μL per mg tissue, to each tube. The sample was homogenized again for metabolite extraction using the same setup for 1 min twice, followed by sonication in an ice-water bath for 5 min. The tube was centrifuged at 15,000 rpm and at 10 0C for 20 min. The clear supernatant was transferred to a 1.5-mL Eppendorf tube. A 60-μL aliquot from each sample was dried down inside the same nitrogen evaporator and the residue was reconstituted in 40 μL of 80% methanol. 10 μL was injected for reversed-phase (RP)-UPLC-FTMS. Two rounds of sample injections were made, with positive- and negative-ion detection, respectively. |
Chromatography:
| Chromatography ID: | CH001672 |
| Instrument Name: | Thermo Dionex Ultimate 3000 |
| Column Name: | Waters BEH C8 (50 x 2.1mm,1.7um) |
| Chromatography Type: | Reversed phase |
Analysis:
| Analysis ID: | AN002273 |
| Analysis Type: | MS |
| Chromatography ID: | CH001672 |
| Num Factors: | 3 |
| Has Mz: | 1 |
| Has Rt: | 1 |
| Rt Units: | Minutes |
| Results File: | ST001366_AN002273_Results.txt |
| Units: | abundance |
| Analysis ID: | AN002274 |
| Analysis Type: | MS |
| Chromatography ID: | CH001672 |
| Num Factors: | 3 |
| Has Mz: | 1 |
| Has Rt: | 1 |
| Rt Units: | Minutes |
| Results File: | ST001366_AN002274_Results.txt |
| Units: | abundance |
