Metabolomics Workbench : NIH Data Repository

MB Sample ID: SA047737

Local Sample ID:	ms6120-8
Subject ID:	SU000890
Subject Type:	Mouse
Subject Species:	Mus musculus
Taxonomy ID:	10090
Species Group:	Mammal

Select appropriate tab below to view additional metadata details:

Subject:

Subject ID:	SU000890
Subject Type:	Mouse
Subject Species:	Mus musculus
Taxonomy ID:	10090
Species Group:	Mammal

Factors:

Local Sample ID	MB Sample ID	Factor Level ID	Level Value	Factor Name
ms6120-8	SA047737	FL009384	P60	Time
ms6120-8	SA047737	FL009384	PAR2	Group

Collection:

Collection ID:	CO000884
Collection Summary:	This prior project involved frozen whole mouse spinal cord (SC) samples for Untargeted Profiling (unbiased metabolomics assay). There were 9 samples total, n=3 for each genotype that includes wild type control, PAR1 KO and PAR2 KO at P60 days. Your team prepared the samples and ran the profiling and provided us with the results. Since the outcome of this preliminary study using 3 animals for each genotype looked so promising, we discussed bringing the total number to 5 and re-running to improve the power. Therefore, we are submitting 2 more samples for each genotype at P60. In addition, we are providing 5 samples for each genotype at P21 (an earlier age) for additional comparisons. To bring n=5 for each P60 genotype we provide 2 more samples per genotype. In addition we provide n=5 for P21 for each genotype (wild type, PAR1 and PAR2).
Sample Type:	Spinal cord

Treatment:

Treatment ID:	TR000904
Treatment Summary:	A 3g Clip produces moderate SCI including demyelination and clinical impairment and we recently published a detailed methodology. At 1 week after injury, the 3g injured mice are expected to have an average Basso Mouse Scale score (BMS)=5 on a 9 point scale such that they have frequent plantar stepping with no or some coordination. This level of impairment was chosen to provide a sufficient window to observe recovery.

Treatment ID:

TR000904

Treatment Summary:

A 3g Clip produces moderate SCI including demyelination and clinical impairment and we recently published a detailed methodology. At 1 week after injury, the 3g injured mice are expected to have an average Basso Mouse Scale score (BMS)=5 on a 9 point scale such that they have frequent plantar stepping with no or some coordination. This level of impairment was chosen to provide a sufficient window to observe recovery.

Sample Preparation:

Sampleprep ID:	SP000897
Sampleprep Summary:	Cholesterol of mouse spinal cord Lipids will be quantified in myelin isolated in high yield and purity by subcellular fractionation from the lumbosacral spinal cord. While there are no absolutely ‘myelin-specific’ lipids, galactocerebroside is the most typical of myelin in the adult nervous system being directly proportional to the amount of myelin. Sulfatide is another galactolipid enriched in myelin. Together with cholesterol, these form 78% of the total amount of lipid in the myelin membrane and each will be quantified using LC/MS/MS. A highly sensitive assay for galactocerebroside was recently established by the Mayo Metabolomics Core and can be implemented immediately. The LC/MS/MS panel for free fatty acids, including the very long chain fatty acids found in myelin is also routinely performed by the Core. Cholesterol will be quantified using an NMR-based approach by the Mayo Dept. of Laboratory Medicine Clinical Core. Additionally, we have a plan in place with the Metabolomics Core to develop LC/MS/MS assays for sulfatide and sphingomyelin during the Pilot proposal. Having quantitative assays for each of these key myelin lipids will facilitate our goal to comprehensively profile myelin lipid metabolism and will form foundational assays for a future NIH grant focused on myelin metabolism.

Sampleprep ID:

SP000897

Sampleprep Summary:

Cholesterol of mouse spinal cord Lipids will be quantified in myelin isolated in high yield and purity by subcellular fractionation from the lumbosacral spinal cord. While there are no absolutely ‘myelin-specific’ lipids, galactocerebroside is the most typical of myelin in the adult nervous system being directly proportional to the amount of myelin. Sulfatide is another galactolipid enriched in myelin. Together with cholesterol, these form 78% of the total amount of lipid in the myelin membrane and each will be quantified using LC/MS/MS. A highly sensitive assay for galactocerebroside was recently established by the Mayo Metabolomics Core and can be implemented immediately. The LC/MS/MS panel for free fatty acids, including the very long chain fatty acids found in myelin is also routinely performed by the Core. Cholesterol will be quantified using an NMR-based approach by the Mayo Dept. of Laboratory Medicine Clinical Core. Additionally, we have a plan in place with the Metabolomics Core to develop LC/MS/MS assays for sulfatide and sphingomyelin during the Pilot proposal. Having quantitative assays for each of these key myelin lipids will facilitate our goal to comprehensively profile myelin lipid metabolism and will form foundational assays for a future NIH grant focused on myelin metabolism.

Combined analysis:

Analysis ID	AN001388
Analysis type	MS
Chromatography type	GC
Chromatography system	Agilent 7890A
Column	Agilent HP5-MS (30m × 0.25mm, 0.25 um)
MS Type	EI
MS instrument type	Single quadrupole
MS instrument name	Agilent 5975C
Ion Mode	POSITIVE
Units	cholesterol (ug/mg tissue)

Chromatography:

Chromatography ID:	CH000972
Instrument Name:	Agilent 7890A
Column Name:	Agilent HP5-MS (30m × 0.25mm, 0.25 um)
Chromatography Type:	GC

MS:

MS ID:	MS001280
Analysis ID:	AN001388
Instrument Name:	Agilent 5975C
Instrument Type:	Single quadrupole
MS Type:	EI
Ion Mode:	POSITIVE