Summary of Study ST001883

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 PR001187. The data can be accessed directly via it's Project DOI: 10.21228/M88M43 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.

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Study IDST001883
Study TitleMetabolomics of Ndufs4 KO urine (part - I)
Study SummaryUntargeted GC-TOF-MS analysis of Ndufs4 KO and WT mouse urine
Institute
North-West University
Last NameLouw
First NameRoan
AddressHofman Street
EmailRoan.Louw@nwu.ac.za
Phone+27 18 299 4074
Submit Date2021-06-30
Raw Data AvailableYes
Raw Data File Type(s)cdf
Analysis Type DetailGC-MS
Release Date2022-06-30
Release Version1
Roan Louw Roan Louw
https://dx.doi.org/10.21228/M88M43
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR001187
Project DOI:doi: 10.21228/M88M43
Project Title:Ndufs4 KO mouse urine metabolomics
Project Type:Multi-platform metabolomics analysis of Ndufs4 KO mouse urine
Project Summary:Multi-platform metabolomics analysis of urine from the Ndufs4 knockout (Ndufs4-/-) mouse model of human Leigh syndrome
Institute:North-West University
Last Name:Louw
First Name:Roan
Address:Hofman Street
Email:Roan.Louw@nwu.ac.za
Phone:+27 18 299 4074

Subject:

Subject ID:SU001961
Subject Type:Mammal
Subject Species:Mus musculus
Taxonomy ID:10090
Genotype Strain:Ndufs4, https://www.jax.org/strai n/02705 8
Age Or Age Range:45-50 days
Gender:Male
Animal Animal Supplier:Jackson Laboratory (ME, USA)
Animal Light Cycle:12:12 h
Animal Feed:Rodent Breeder, Cat. #RM1845, LabChef, Nutritionhub
Animal Water:ad libitum

Factors:

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

mb_sample_id local_sample_id Genotype
SA17509086_3qKO
SA17509196_2iKO
SA17509220_4mKO
SA1750932_3sKO
SA17509442_4qKO
SA17509568_1oKO
SA17509667_2fKO
SA17509718_2lKO
SA17509860_2eKO
SA1750998_4jKO
SA17510044_3kKO
SA17510169_2fKO
SA17510228_3gKO
SA17510334_4oKO
SA17510450_4sKO
SA1751052_4iKO
SA17510656_2dKO
SA17510789_1rKO
SA17510837_3jKO
SA17510910_1vKO
SA17511033_2oKO
SA17511145_3kKO
SA17511254_4aKO
SA17511362_2tWT
SA1751142_1uWT
SA17511565_3nWT
SA17511611_3dWT
SA17511716_4mWT
SA17511891_2iWT
SA17511962_4bWT
SA17512083_3pWT
SA1751218_1vWT
SA17512227_4nWT
SA17512337_4pWT
SA17512482_2gWT
SA1751259_3dWT
SA17512688_3qWT
SA1751279_4jWT
SA17512849_2aWT
SA17512942_3kWT
SA17513068_3nWT
SA17513165_2uWT
SA17513281_3pWT
SA17513353_2cWT
SA17513429_4nWT
SA17513561_2eWT
SA17513663_4bWT
SA17513787_3qWT
SA17513897_4hWT
SA17513998_4hWT
SA17514054_2cWT
SA17514126_3gWT
SA17514257_3lWT
Showing results 1 to 53 of 53

Collection:

Collection ID:CO001954
Collection Summary:Urine was collected from individual mice in metabolic cages after overnight (12 hours) fasting with ad libitum access to water. Since Ndufs4 KO mice yielded limited urine volumes, urine droplets that failed to reach the collection tube were also collected. Hence, the separating cone, collection funnel and urine collection tubes were all treated with sodium azide (NaN3; 0.1% w/v; WT: 100 μL and KO: 50 μL) to prevent bacterial growth. Samples were snap-frozen in liquid nitrogen upon collection and stored at −80 °C until used.
Sample Type:Urine
Storage Conditions:-80℃

Treatment:

Treatment ID:TR001973
Treatment Summary:The animals did not receive any treatment

Sample Preparation:

Sampleprep ID:SP001967
Sampleprep Summary:Pre-determined volumes of urine, containing 0.0625 μmole creatinine, were supplemented with internal standards and deproteinized using methanol. Urine samples were then dried under nitrogen and derivatized (methoxymated and silylated) prior to analysis.
Sampleprep Protocol Filename:GC_sample_prep_protocol.pdf

Combined analysis:

Analysis ID AN003047
Analysis type MS
Chromatography type GC
Chromatography system Agilent 7890A
Column Restek Rtx-5Sil MS (30 x 0.25mm, 0.25um)
MS Type EI
MS instrument type GC-TOF
MS instrument name Leco GC-TOF
Ion Mode POSITIVE
Units mg/g creatinine

Chromatography:

Chromatography ID:CH002257
Methods Filename:GC_data_acquisition_method.pdf
Instrument Name:Agilent 7890A
Column Name:Restek Rtx-5Sil MS (30 x 0.25mm, 0.25um)
Chromatography Type:GC

MS:

MS ID:MS002834
Analysis ID:AN003047
Instrument Name:Leco GC-TOF
Instrument Type:GC-TOF
MS Type:EI
MS Comments:The LECO Corporation ChromaTOF® software (v 4.5x) was used for data acquisition and extraction. This included automatic baseline removal via the “spanning” tracking method (offset of 1; just above the noise) and auto smoothing, with the software’s Statistical Compare feature used to align peaks. Spectral matching was done using the NIST11 commercial library and an in-house mass spectral library in order to identify important analytes.
Ion Mode:POSITIVE
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