Summary of Study ST001483

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.


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Study IDST001483
Study TitleMetabolomics of Ndufs4 KO brain regions (part - III)
Study SummaryTargeted LC-MS/MS analysis of amino acids and acylcarnitines in Ndufs4 KO and WT mouse brain stem (BST)
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)d
Analysis Type DetailLC-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:SU001557
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
SA125146BST1 15 (15)KO
SA125147BST1 16 (16)KO
SA125148BST1 21 (21)KO
SA125149BST1 12 (14)KO
SA125150BST1 19 (19)KO
SA125151BST1 5 (24)KO
SA125152BST1 1 (E1)KO
SA125153BST1 2 (E2)KO
SA125154BST1 4 (E4)KO
SA125155BST2 27 (27)KO
SA125156BST1 9 (10)KO
SA125157BST2 29 (29)KO
SA125158BST2 40 (41)KO
SA125159BST2 45 (3)KO
SA125160BST2 41 (42) redoKO
SA125161BST2 38 (38)KO
SA125162BST2 37 (36)KO
SA125163BST2 31 (34)KO
SA125164BST2 32 (32)KO
SA125165BST2 33 (33)KO
SA125166BST2 35 (35)KO
SA125167BST2 47 (5)WT
SA125168BST2 46 (4)WT
SA125169BST2 44 (2)WT
SA125170BST1 14 (13)WT
SA125171BST1 18 (18)WT
SA125172BST1 20 (20)WT
SA125173BST1 21 (17) redoWT
SA125174BST1 13 (12)WT
SA125175BST1 11 (11)WT
SA125176BST1 6 (E6)WT
SA125177BST1 7 (7)WT
SA125178BST1 8 (8)WT
SA125179BST1 10 (9)WT
SA125180BST1 22 (22)WT
SA125181BST1 23 (23)WT
SA125182BST2 39 (39)WT
SA125183BST2 39 (39) after cleanWT
SA125184BST2 42 (40)WT
SA125185BST2 43 (1)WT
SA125186BST2 36 (37)WT
SA125187BST2 34 (31)WT
SA125188BST2 25 (25)WT
SA125189BST2 26 (26)WT
SA125190BST2 28 (28)WT
SA125191BST2 30 (30)WT
SA125192BST1 3 (E3)WT
Showing results 1 to 47 of 47


Collection ID:CO001552
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:TR001572
Treatment Summary:The animals did not receive any treatment

Sample Preparation:

Sampleprep ID:SP001565
Sampleprep Summary:Brain regions were homogenized in the presence of internal standards using a vibration mill. Metabolite extraction was achieved using a biphasic Bligh–Dyer extraction method (methanol/water/chloroform, 2:1.8:2). The polar phases of biphasic extracts were used for LC-MS/MS analysis
Sampleprep Protocol Filename:GC_sample_prep_protocol.pdf

Combined analysis:

Analysis ID AN002460
Analysis type MS
Chromatography type Reversed phase
Chromatography system Agilent 1200
Column Agilent C18 Zorbax SB-AQ (150 x 2.1mm,3.5 um)
MS instrument type Triple quadrupole
MS instrument name Agilent 6410A QQQ
Units Area


Chromatography ID:CH001802
Instrument Name:Agilent 1200
Column Name:Agilent C18 Zorbax SB-AQ (150 x 2.1mm,3.5 um)
Chromatography Type:Reversed phase


MS ID:MS002280
Analysis ID:AN002460
Instrument Name:Agilent 6410A QQQ
Instrument Type:Triple quadrupole
MS Comments:The Agilent© MassHunter Workstation (v B02.01) and MassHunter Optimiser (v B02.01) software were used for data acquisition in the multiple reaction monitoring (MRM) configuration setting with parameters set for target amino acids, -derivatives, acylcarnitines, and isotopes. Data extraction was done using the Agilent© MassHunter Workstation software (v B06.00; Qualitative Analysis and Quantitative Analysis)