Summary of Study ST000222
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 PR000182. The data can be accessed directly via it's Project DOI: 10.21228/M8M888 This work is supported by NIH grant, U2C- DK119886.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
| Study ID | ST000222 |
| Study Title | Bile acid targeted metabolomics of the small intestine in malnourished and control mice |
| Study Type | Targeted metabolomics |
| Study Summary | A total of 8 samples from 6 week old, female C57BL/6 mice, treated for 3 weeks with a malnourished diet or a control-fed isocaloric diet. Samples were taken from the small intestinal fecal content at the terminus of the ileum for targeted bile acid analysis. |
| Institute | University of Victoria |
| Department | The Uvic Proteomics and Metabolomics Innovation Centre |
| Last Name | Borchers |
| First Name | Christoph |
| Address | #3101-4464 Markham St Victoria, BC Canada, V8Z 7X8 |
| christoph@proteincentre.com | |
| Submit Date | 2015-06-08 |
| Num Groups | 2 |
| Total Subjects | 8* |
| Study Comments | *One sample failed quality control in the malnourished group, thus was not included in the study |
| Raw Data Available | Yes |
| Raw Data File Type(s) | wiff |
| Uploaded File Size | 4.0 M |
| Analysis Type Detail | LC-MS |
| Release Date | 2015-06-08 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR000182 |
| Project DOI: | doi: 10.21228/M8M888 |
| Project Title: | Metabolomic analysis of the small intestinal content of malnourished mice |
| Institute: | University of British Columbia |
| Department: | Microbiology and Immunology |
| Laboratory: | Dr. B. Brett Finlay |
| Last Name: | Finlay |
| First Name: | Brett |
| Address: | 2185 East Mall, Vancouver, BC, Canada V6T 1Z4 |
| Email: | bfinlay@msl.ubc.ca |
| Funding Source: | Canadian Institutes for Health Research |
Subject:
| Subject ID: | SU000241 |
| Subject Type: | Animal |
| Subject Species: | Mus musculus |
| Taxonomy ID: | 10090 |
| Genotype Strain: | C57BL/6 |
| Age Or Age Range: | 6 weeks at collection |
| Gender: | Female |
| Animal Animal Supplier: | Jackson Labs |
| Animal Housing: | Conventional |
| Animal Feed: | Low Protein, Low Fat Malnourished Diet/Isocaloric Control Diet |
| Cell Primary Immortalized: | Malnourished/Control |
| Species Group: | Mammal |
Factors:
Subject type: Animal; Subject species: Mus musculus (Factor headings shown in green)
| mb_sample_id | local_sample_id | Diet |
|---|---|---|
| SA010740 | CON2 | control |
| SA010741 | CON3 | control |
| SA010742 | CON4 | control |
| SA010743 | CON1 | control |
| SA010744 | MAL4 | malnourished |
| SA010745 | MAL2 | malnourished |
| SA010746 | MAL3 | malnourished |
| SA010747 | MAL1 | malnourished |
| Showing results 1 to 8 of 8 |
Collection:
| Collection ID: | CO000229 |
| Collection Summary: | - |
| Sample Type: | Small intestinal fecal contents |
| Collection Time: | 6 weeks of age |
| Storage Conditions: | -80 degrees |
| Tissue Cell Quantity Taken: | 15-40mg |
Treatment:
| Treatment ID: | TR000249 |
| Treatment Summary: | 4 mice were given a malnourished diet and 4 mice were untreated, fed a control diet |
Sample Preparation:
| Sampleprep ID: | SP000243 |
| Sampleprep Summary: | Bile-acid targeted metabolomics. Each sample was homogenized in LC-MS grade water at a ratio of 150 ?L per 10 mg raw material and with the aid of 5-mm stainless steel metal balls. Bile acids were extracted by addition of acetonitrile at a ratio of 350 ?L per 10 mg raw material followed by vortexing and sonication (1 min) in an ice-water ultrasonic bath. The samples were centrifuged. 20 ?L of the supernatants were precisely taken out and mixed with a predefined mix of 14 deuterium-labeled bile acids as the internal standards. The mixtures were subjected to phospholipid-depletion solid-phase extraction according to a validated protocol for sample cleanup and bile acid enrichment62. The flow-through fractions were collected and then dried under a gentle nitrogen flow. The dried residues were dissolved in 200 ?L of 50% methonal. 10 ?L were injected for quantitation by UPLC-MRM/MS. A Dionex UPLC system was connected to an AB Sciex 4000 QTRAP mass spectrometer which was operated in the negative ion multiple-reaction monitoring (MRM) mode and with electrospray ionization. UPLC separation was carried out on a 15 cm long C-18 UPLC column with water-acetonitrile-formic acid as the mobile phase for binary gradient elution using a developed and validated protocol for comprehensive analysis of bile acids in biological samples (Han, etc. manuscript submitted to Analytical Chemistry). The column temperature was 45 oC and the flow rate was 0.35 mL/min. 45 bile acids (including the 19 targeted bile acids) were involved in the quantitation by UPLC/scheduled MRM/MS. Concentrations of the detected bile acids were calculated with internal standard calibration from the linearly regressed standard calibration curves of individual bile acids. The lower limits of quantitation were 0.08 nmoles/mg for all the bile acids. |
Combined analysis:
| Analysis ID | AN000331 |
|---|---|
| Analysis type | MS |
| Chromatography type | |
| Chromatography system | |
| Column | |
| MS Type | ESI |
| MS instrument type | Triple quadrupole |
| MS instrument name | ABI Sciex API 4000 QTrap |
| Ion Mode | NEGATIVE |
| Units | nM/mg |
Chromatography:
| Chromatography ID: | CH000248 |
MS:
| MS ID: | MS000280 |
| Analysis ID: | AN000331 |
| Instrument Name: | ABI Sciex API 4000 QTrap |
| Instrument Type: | Triple quadrupole |
| MS Type: | ESI |
| Ion Mode: | NEGATIVE |
