Summary of Study ST001486

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench,, 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.


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 IDST001486
Study TitleMetabolomics of Ndufs4 KO brain regions (part - VI)
Study SummaryUntargeted GC-TOF-MS analysis of Ndufs4 KO and WT mouse cerebellum (CB)
North-West University
Last NameLouw
First NameRoan
AddressHofman Street
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 application/zip

Select appropriate tab below to view additional metadata details:


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
Phone:+27 18 299 4074


Subject ID:SU001560
Subject Type:Mammal
Subject Species:Mus musculus
Taxonomy ID:10090
Genotype Strain:Ndufs4, n/02705 8
Age Or Age Range:45-50 days
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


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

mb_sample_id local_sample_id Genotype
SA125286CBA 15 (35)KO
SA125287CBA 20 (14)KO
SA125288CBA 23 (38)KO
SA125289CBA 13 (34)KO
SA125290CBA 21 (36)KO
SA125291CBA 8 (33)KO
SA125292CBA 3 (27)KO
SA125293CBA 5 (29)KO
SA125294CBA 7 (32)KO
SA125295CBB 26 (41)KO
SA125296CBA 11 (3)KO
SA125297CBB 27 (42)KO
SA125298CBB 37 (16)KO
SA125299CBB 40 (19)KO
SA125300CBB 42 (21)KO
SA125301CBB 45 (24)KO
SA125302CBB 36 (15)KO
SA125303CBB 33 (E5)KO
SA125304CBB 29 (E1)KO
SA125305CBB 30 (E2)KO
SA125306CBB 32 (E4)KO
SA125307CBB 44 (23)WT
SA125308CBB 43 (22)WT
SA125309CBA 14 (5)WT
SA125310CBA 16 (7)WT
SA125311CBA 17 (8)WT
SA125312CBA 18 (9)WT
SA125313CBA 12 (4)WT
SA125314CBA 10 (2)WT
SA125315CBA 2 (26)WT
SA125316CBA 4 (28)WT
SA125317CBA 6 (30)WT
SA125318CBA 9 (1)WT
SA125319CBA 19 (11)WT
SA125320CBA 22 (37)WT
SA125321CBB 35 (13)WT
SA125322CBB 38 (17)WT
SA125323CBB 39 (18)WT
SA125324CBB 41 (20)WT
SA125325CBB 34 (12)WT
SA125326CBB 31 (E3)WT
SA125327CBB 24 (39) regWT
SA125328CBB 25 (40)WT
SA125329CBB 28 (E6)WT
SA125330CBA 1 (25)WT
Showing results 1 to 45 of 45


Collection ID:CO001555
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 ID:TR001575
Treatment Summary:The animals did not receive any treatment

Sample Preparation:

Sampleprep ID:SP001568
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

Combined analysis:

Analysis ID AN002463
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
Units Area


Chromatography ID:CH001805
Instrument Name:Agilent 7890A
Column Name:Restek Rtx-5Sil (30m x 0.25mm,0.25um)
Chromatography Type:GC


MS ID:MS002283
Analysis ID:AN002463
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.
Analysis Protocol File:Data_processing_method.pdf