Summary of Study ST001484

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 PR001003. The data can be accessed directly via it's Project DOI: 10.21228/M8210V 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 IDST001484
Study TitleMetabolomics of Ndufs4 KO brain regions (part - IV)
Study SummaryUntargeted GC-TOF-MS analysis of Ndufs4 KO and WT mouse brain stem (BST)
Institute
North-West University
Last NameLouw
First NameRoan
AddressHofman Street
EmailRoan.Louw@nwu.ac.za
Phone+27 18 299 4074
Submit Date2020-09-11
Raw Data AvailableYes
Raw Data File Type(s)peg
Analysis Type DetailGC-MS
Release Date2021-09-10
Release Version1
Roan Louw Roan Louw
https://dx.doi.org/10.21228/M8210V
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR001003
Project DOI:doi: 10.21228/M8210V
Project Title:Ndufs4 KO mouse model metabolomics studies
Project Type:Multi-platform metabolomics analysis
Project Summary:Multi-platform metabolomics analysis of tissues and biofluids 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:SU001558
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
SA125193BST1 21KO
SA125194BST1 24KO
SA125195BST2 29KO
SA125196BST1 19KO
SA125197BST2 27KO
SA125198BST1 15KO
SA125199BST1 3KO
SA125200BST1 10KO
SA125201BST1 14KO
SA125202BST2 32KO
SA125203BST1 16KO
SA125204BST2 33KO
SA125205BST2 42KO
SA125206BST2 E 1KO
SA125207BST2 E 2KO
SA125208BST2 E 4KO
SA125209BST2 41KO
SA125210BST2 38KO
SA125211BST2 34KO
SA125212BST2 35KO
SA125213BST2 36KO
SA125214BST2 E 6WT
SA125215BST2 E 3WT
SA125216BST1 11WT
SA125217BST1 12WT
SA125218BST1 13WT
SA125219BST1 17WT
SA125220BST1 9WT
SA125221BST1 8WT
SA125222BST1 2WT
SA125223BST1 4WT
SA125224BST1 5WT
SA125225BST1 7WT
SA125226BST1 18WT
SA125227BST1 20WT
SA125228BST2 31WT
SA125229BST2 37WT
SA125230BST2 39WT
SA125231BST2 40WT
SA125232BST2 30WT
SA125233BST2 28WT
SA125234BST1 22WT
SA125235BST1 23WT
SA125236BST2 25WT
SA125237BST2 26WT
SA125238BST1 1WT
Showing results 1 to 46 of 46

Collection:

Collection ID:CO001553
Collection Summary:Mice were euthanized between postnatal day (P) 45-50 via cervical dislocation at the same time of day (8:00-9:00 AM) after overnight (12-h) fasting. The brain was removed and rinsed with saline solution (SABAX PBS; 0.9% NaCl (w/v), #7634, Adcock Ingram) to remove surrounding blood. The brain regions of interest, namely the anterior cortex (AC), brainstem (BS), cerebellum (CB) and olfactory bulbs (OB), were then dissected, snap-frozen in liquid nitrogen (within 15 minutes postmortem) and stored at − 80°C until used.
Sample Type:Brain

Treatment:

Treatment ID:TR001573
Treatment Summary:The animals did not receive any treatment

Sample Preparation:

Sampleprep ID:SP001566
Sampleprep Summary:Brain regions were homogenized in the presence of internal standards using a vibration mill. Metabolite extraction was achieved using a modified monophasic Bligh–Dyer extraction method with a solvent ratio of 3:1:1 (methanol:water:chloroform).
Sampleprep Protocol Filename:GC_sample_prep_protocol.pdf
Data_processing_method.pdf

Combined analysis:

Analysis ID AN002461
Analysis type MS
Chromatography type GC
Chromatography system Agilent 7890A
Column Restek Rtx-5Sil (30m x 0.25mm,0.25um)
MS Type EI
MS instrument type GC-TOF
MS instrument name Leco Pegasus HT TOF
Ion Mode POSITIVE
Units Area

Chromatography:

Chromatography ID:CH001803
Instrument Name:Agilent 7890A
Column Name:Restek Rtx-5Sil (30m x 0.25mm,0.25um)
Chromatography Type:GC

MS:

MS ID:MS002281
Analysis ID:AN002461
Instrument Name:Leco Pegasus HT 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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