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.

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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.

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Study IDST003549
Study TitleMetabolomics analysis of kidney, brain, liver, and plasma from Aldh7a1-/- and Aldh7a1+/+ mice.
Study SummaryMetabolite 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
DepartmentBiochemistry & Molecular Biology
LaboratoryParker laboratory
Last NameParker
First NameSeth
Address950 W 28th Ave, Vancouver, British Columbia, V6H 0B3, Canada
Emailseth.parker@bcchr.ca
Phone6048753121
Submit Date2024-11-01
Raw Data AvailableYes
Raw Data File Type(s)raw(Thermo)
Analysis Type DetailLC-MS
Release Date2024-11-15
Release Version1
Seth Parker Seth Parker
https://dx.doi.org/10.21228/M86527
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR002185
Project DOI:doi: 10.21228/M86527
Project Title:Metabolomics analysis of tissues isolated from Aldh7a1+/+ and Aldh7a1-/- (KO) mice.
Project Type:Manuscript
Project Summary:ALDH7A1 is an enzyme involved in the catabolism of lysine. Using Aldh7a1-knockout (-/-) and wild-type (+/+) mice and metabolomics, we aim to determine how Aldh7a1-deficiency leads to the accumulation of lysine catabolites upstream of ALDH7A1 and affects other metabolic pathways. Our results suggest that there is a tissue-specific accumulation of lysine and other metabolites, with the brain exhibiting the largest number of significantly different metabolites.
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
Email:seth.parker@bcchr.ca
Phone:6048753121

Subject:

Subject ID:SU003678
Subject Type:Mammal
Subject Species:Mus musculus
Taxonomy ID:10090
Age Or Age Range:15-17 week old mice.
Gender:Male and female
Animal Feed:0.9% w/w lysine, 18 ppm pyridoxine (standard diets)
Species Group:Mammals

Factors:

Subject type: Mammal; Subject species: Mus musculus (Factor headings shown in green)

mb_sample_id local_sample_id Genotype Sample source
SA387804Brain_4Aldh7a1+/+ Brain
SA387805Brain_5Aldh7a1+/+ Brain
SA387806Brain_6Aldh7a1+/+ Brain
SA387816Brain_1Aldh7a1-/- Brain
SA387817Brain_2Aldh7a1-/- Brain
SA387818Brain_3Aldh7a1-/- Brain
SA387807Kidney_4Aldh7a1+/+ Kidney
SA387808Kidney_5Aldh7a1+/+ Kidney
SA387809Kidney_6Aldh7a1+/+ Kidney
SA387819Kidney_3Aldh7a1-/- Kidney
SA387820Kidney_2Aldh7a1-/- Kidney
SA387821Kidney_1Aldh7a1-/- Kidney
SA387810Liver_4Aldh7a1+/+ Liver
SA387811Liver_6Aldh7a1+/+ Liver
SA387812Liver_5Aldh7a1+/+ Liver
SA387822Liver_3Aldh7a1-/- Liver
SA387823Liver_2Aldh7a1-/- Liver
SA387824Liver_1Aldh7a1-/- Liver
SA387813Plasma_6Aldh7a1+/+ Plasma
SA387814Plasma_5Aldh7a1+/+ Plasma
SA387815Plasma_4Aldh7a1+/+ Plasma
SA387825Plasma_1Aldh7a1-/- Plasma
SA387826Plasma_2Aldh7a1-/- Plasma
SA387827Plasma_3Aldh7a1-/- Plasma
Showing results 1 to 24 of 24

Collection:

Collection ID:CO003671
Collection Summary:Liver, brain, or plasma samples collected from mice were snap frozen in liquid nitrogen and ground to a fine powder using a liquid nitrogen cooled mortar and pestle. Metabolites from 25 mg of tissues were extracted using a bead mill and 1 mL of 80% methanol containing internal isotopic standards. 10 µL of plasma was added to 250 µL of 80% methanol containing internal isotopic standards. All samples were analyzed using LCMS.
Sample Type:Tissue or Plasma

Treatment:

Treatment ID:TR003687
Treatment Summary:No treatment.

Sample Preparation:

Sampleprep ID:SP003685
Sampleprep Summary:Dried samples were reconstituted in 50 µL of HPLC-grade water. Samples were vortexed for ~10 minutes, then centrifuged at 21,000 x g for 15 min at 4°C. 40 microliters were transferred to LC vials containing glass inserts for analysis.

Chromatography:

Chromatography ID:CH004432
Instrument Name:Thermo Vanquish
Column Name:Merck SeQuant ZIC-pHILIC (150 x 2.1mm,5um)
Column Temperature:25°C
Flow Gradient:80-20%B (0-30 min), 20-20%B (30-40 minute), and 20-80%B (40-40.5 minute); the LC column was re-equilibrated using 80-80%B from 40.5-52 minute before subsequent injections
Flow Rate:100 uL/min
Solvent A:100% Water; 10 mM Ammonium Carbonate, pH 9.0
Solvent B:100% Acetonitrile
Chromatography Type:HILIC

Analysis:

Analysis ID:AN005833
Analysis Type:MS
Chromatography ID:CH004432
Num Factors:8
Num Metabolites:207
Rt Units:Minutes
Units:Ion counts
  
Analysis ID:AN005834
Analysis Type:MS
Chromatography ID:CH004432
Num Factors:8
Num Metabolites:207
Rt Units:Minutes
Units:Ion counts
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