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MB Sample ID: SA048396
| Local Sample ID: | nhilic-9jun16-003-r001 |
| Subject ID: | SU000896 |
| 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: | SU000896 |
| 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 |
|---|---|---|---|---|
| nhilic-9jun16-003-r001 | SA048396 | FL009534 | K6+/+ | Group |
| nhilic-9jun16-003-r001 | SA048396 | FL009534 | P21 | Time point |
| nhilic-9jun16-003-r001 | SA048396 | FL009534 | 1 | rep |
Collection:
| Collection ID: | CO000890 |
| Collection Summary: | Tissue is from adult mouse spinal cord (SC). We are submitting these samples for Untargeted Profiling (unbiased metabolomics assay) and for lipid analysis. The lipid assays we request are 1) free fatty acid composition of lipids; 2) free fatty acid panel; 3) cholesterol concentration (free and bound); 4) Ceramides, including galactosyl and glucosyl; 5) sphingomyelin. The Untargeted profiling is our top priority, followed by the lipid assays as listed. All samples were snap frozen at the point of harvest and approximate weights are provided. The samples are submitted as intact pieces of tissue. There are two different genotypes (K6+/+ and K6-/-) and 20 samples total, n=5 for each group that includes P21(K6+/+); P90 (K6+/+); P21 (K6-/-); and P90 (K6-/-). We would like to make comparisons across the 4 groups. |
| Sample Type: | Spinal cord |
Treatment:
| Treatment ID: | TR000910 |
| 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: | SP000903 |
| Sampleprep Summary: | large scale profiling 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 | AN001399 | AN001400 | AN001401 |
|---|---|---|---|
| Analysis type | MS | MS | MS |
| Chromatography type | Reversed phase | HILIC | HILIC |
| Chromatography system | Agilent 1290 Infinity | Agilent 1290 Infinity | Agilent 1290 Infinity |
| Column | Waters Acquity HSS C18 (150 x 2.1mm,1.8um) | Waters Acquity BEH Amide (150 x 2.1mm,1.7um) | Waters Acquity BEH Amide (150 x 2.1mm,1.7um) |
| MS Type | ESI | ESI | ESI |
| MS instrument type | QTOF | QTOF | QTOF |
| MS instrument name | Agilent 6550 QTOF | Agilent 6550 QTOF | Agilent 6550 QTOF |
| Ion Mode | NEGATIVE | POSITIVE | NEGATIVE |
| Units | intensity | intensity | intensity |
Chromatography:
| Chromatography ID: | CH000980 |
| Instrument Name: | Agilent 1290 Infinity |
| Column Name: | Waters Acquity HSS C18 (150 x 2.1mm,1.8um) |
| Chromatography Type: | Reversed phase |
| Chromatography ID: | CH000981 |
| Instrument Name: | Agilent 1290 Infinity |
| Column Name: | Waters Acquity BEH Amide (150 x 2.1mm,1.7um) |
| Chromatography Type: | HILIC |
MS:
| MS ID: | MS001291 |
| Analysis ID: | AN001399 |
| Instrument Name: | Agilent 6550 QTOF |
| Instrument Type: | QTOF |
| MS Type: | ESI |
| Ion Mode: | NEGATIVE |
| MS ID: | MS001292 |
| Analysis ID: | AN001400 |
| Instrument Name: | Agilent 6550 QTOF |
| Instrument Type: | QTOF |
| MS Type: | ESI |
| Ion Mode: | POSITIVE |
| MS ID: | MS001293 |
| Analysis ID: | AN001401 |
| Instrument Name: | Agilent 6550 QTOF |
| Instrument Type: | QTOF |
| MS Type: | ESI |
| Ion Mode: | NEGATIVE |
