Summary of study ST001481

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 IDST001481
Study TitleMetabolomics of Ndufs4 KO brain regions (part - II)
Study SummaryTargeted LC-MS/MS analysis of amino acids and acylcarnitines in Ndufs4 KO and WT mouse anterior cortex (AC)
Institute
North-West University
Last NameLouw
First NameRoan
AddressHofman Street
EmailRoan.Louw@nwu.ac.za
Phone+27 18 299 4074
Submit Date2020-09-10
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:SU001555
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
SA125025AC1 21KO
SA125026AC1 24KO
SA125027AC2 29KO
SA125028AC1 19KO
SA125029AC2 27KO
SA125030AC1 15KO
SA125031AC1 3KO
SA125032AC1 10KO
SA125033AC1 14KO
SA125034AC2 32KO
SA125035AC1 16KO
SA125036AC2 33KO
SA125037AC2 42KO
SA125038AC2 E 1KO
SA125039AC2 E 2KO
SA125040AC2 E 5KO
SA125041AC2 41KO
SA125042AC2 38KO
SA125043AC2 34KO
SA125044AC2 35KO
SA125045AC2 36KO
SA125046AC2 E 6WT
SA125047AC2 E 3WT
SA125048AC1 11WT
SA125049AC1 12WT
SA125050AC1 13WT
SA125051AC1 17WT
SA125052AC1 9WT
SA125053AC1 8WT
SA125054AC1 2WT
SA125055AC1 4WT
SA125056AC1 5WT
SA125057AC1 7WT
SA125058AC1 18WT
SA125059AC1 20WT
SA125060AC2 31WT
SA125061AC2 37WT
SA125062AC2 39WT
SA125063AC2 40WT
SA125064AC2 30WT
SA125065AC2 28WT
SA125066AC1 22WT
SA125067AC1 23WT
SA125068AC2 25WT
SA125069AC2 26WT
SA125070AC1 1WT
Showing results 1 to 46 of 46

Collection:

Collection ID:CO001550
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:TR001570
Treatment Summary:The animals did not receive any treatment

Sample Preparation:

Sampleprep ID:SP001563
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 AN002458
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 Pegasus HT TOF
Ion Mode POSITIVE
Units Area

Chromatography:

Chromatography ID:CH001800
Instrument Name:Agilent 7890A
Column Name:Restek Rtx-5Sil MS (30 x 0.25mm, 0.25um)
Chromatography Type:GC

MS:

MS ID:MS002278
Analysis ID:AN002458
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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