Summary of Study ST003549
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 PR002185. The data can be accessed directly via it's Project DOI: 10.21228/M86527 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 | ST003549 |
| Study Title | Metabolomics analysis of kidney, brain, liver, and plasma from Aldh7a1-/- and Aldh7a1+/+ mice. |
| Study Summary | Metabolite analysis of kidney, brain, liver, and plasma isolated from Aldh7a1+/+ and Aldh7a1-/- (n=3/each) fed diets consisting of 0.9% w/w lysine and 18 ppm pyridoxine. Tissues were cryo-homogenized using a liquid nitrogen cooled mortar and pestle into a fine powder and approximately 25-50 mg of each tissue was transferred to a pre-weighed homogenization tube to which ~20 2.3 mm zirconia beads and 1 mL of 80% ice cold methanol were added. Tissues were homogenized using a bead mill and cleared by centrifugation at 4C, where each of the 3-4 cycles consisted of a 60 second homogenization at 6 m/s followed by a 30 second pause. A volume equivalent to 25 mg of tissue extract was transferred to a new tube, and 250 µL of 80% methanol containing 1 µL of stable isotope-labeled internal amino acid standard mix was added. Metabolites were concentrated using a SpeedVac until dry. For plasma metabolite analysis, 10 µL of plasma was added to 250 µl of 80% methanol containing 1 µL of stable isotope-labeled internal amino acid standard mix, vortexed at 4C for 10 minutes, and centrifuged. 0.9 mL of supernatant was transferred to a new tube and concentrated using a SpeedVac until dry. Metabolites were reconstituted into 25-50 µL of water, vortexed, centrifuged, and transferred to vials for analysis by LCMS. LCMS was performed using a ZIC-pHILIC LC column coupled to a Vanquish LC and a flow gradient consisting of 10 mM ammonium carbonate in water and pure acetonitrile. The LC was coupled to an Exploris 240 mass spectrometer operated in a polarity switching data-dependent Top 5 mode. Full MS scan parameters for both positive and negative mode were set to 67-1000 m/z at a resolution of 120k and ddMS2 were collected at a resolution of 30k. Data files are labeled with brain, liver, kidney, and plasma followed by a number. The number represents a mouse. Samples 1-3 are from Aldh7a1-/- mice and samples 4-6 are from Aldh7a1+/+ mice. |
| Institute | University of British Columbia |
| Department | Biochemistry & Molecular Biology |
| Laboratory | Parker laboratory |
| Last Name | Parker |
| First Name | Seth |
| Address | 950 W 28th Ave, Vancouver, British Columbia, V6H 0B3, Canada |
| seth.parker@bcchr.ca | |
| Phone | 6048753121 |
| Submit Date | 2024-11-01 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | raw(Thermo) |
| Analysis Type Detail | LC-MS |
| Release Date | 2024-11-15 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Factors:
Subject type: Mammal; Subject species: Mus musculus (Factor headings shown in green)
| mb_sample_id | local_sample_id | Genotype | Sample source |
|---|---|---|---|
| SA387804 | Brain_4 | Aldh7a1+/+ | Brain |
| SA387805 | Brain_5 | Aldh7a1+/+ | Brain |
| SA387806 | Brain_6 | Aldh7a1+/+ | Brain |
| SA387816 | Brain_1 | Aldh7a1-/- | Brain |
| SA387817 | Brain_2 | Aldh7a1-/- | Brain |
| SA387818 | Brain_3 | Aldh7a1-/- | Brain |
| SA387807 | Kidney_4 | Aldh7a1+/+ | Kidney |
| SA387808 | Kidney_5 | Aldh7a1+/+ | Kidney |
| SA387809 | Kidney_6 | Aldh7a1+/+ | Kidney |
| SA387819 | Kidney_3 | Aldh7a1-/- | Kidney |
| SA387820 | Kidney_2 | Aldh7a1-/- | Kidney |
| SA387821 | Kidney_1 | Aldh7a1-/- | Kidney |
| SA387810 | Liver_4 | Aldh7a1+/+ | Liver |
| SA387811 | Liver_6 | Aldh7a1+/+ | Liver |
| SA387812 | Liver_5 | Aldh7a1+/+ | Liver |
| SA387822 | Liver_3 | Aldh7a1-/- | Liver |
| SA387823 | Liver_2 | Aldh7a1-/- | Liver |
| SA387824 | Liver_1 | Aldh7a1-/- | Liver |
| SA387813 | Plasma_6 | Aldh7a1+/+ | Plasma |
| SA387814 | Plasma_5 | Aldh7a1+/+ | Plasma |
| SA387815 | Plasma_4 | Aldh7a1+/+ | Plasma |
| SA387825 | Plasma_1 | Aldh7a1-/- | Plasma |
| SA387826 | Plasma_2 | Aldh7a1-/- | Plasma |
| SA387827 | Plasma_3 | Aldh7a1-/- | Plasma |
| Showing results 1 to 24 of 24 |
