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MB Sample ID: SA169097
| Local Sample ID: | PVC11 |
| Subject ID: | SU001896 |
| Subject Type: | Mammal |
| Subject Species: | Mus musculus |
| Taxonomy ID: | 10090 |
| Age Or Age Range: | 14-15 month-old |
| Gender: | Male |
Select appropriate tab below to view additional metadata details:
Subject:
| Subject ID: | SU001896 |
| Subject Type: | Mammal |
| Subject Species: | Mus musculus |
| Taxonomy ID: | 10090 |
| Age Or Age Range: | 14-15 month-old |
| Gender: | Male |
Factors:
| Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
|---|---|---|---|---|
| PVC11 | SA169097 | FL020175 | PVC | Region |
| PVC11 | SA169097 | FL020175 | E3/4 | Genotype |
Collection:
| Collection ID: | CO001889 |
| Collection Summary: | Mice were sacrificed by cervical dislocation to maintain the brain environment, and individual brain regions were immediately removed and snap-frozen on dry ice. Tissues were stored at -80°C for prior to extraction. |
| Sample Type: | Brain |
Treatment:
| Treatment ID: | TR001909 |
| Treatment Summary: | No treatments were made. Mice were either APOE3/3, APOE3/4 or APOE4/4 gentoype. |
Sample Preparation:
| Sampleprep ID: | SP001902 |
| Sampleprep Summary: | Lipid and small-molecule metabolite extraction was performed using a methyl tert-butyl ether (MTBE)/methanol extraction protocol modified from previous reports (40, 41), as we have described previously (34). Briefly, individual EC or PVC tissues were homogenized in 400 ul of ice-cold methanol using a bead mill homogenizer (TissueLyser II, Qiagen) at 25 beats/sec, 2x for 45 sec each. Following homogenization, samples were incubated in 1200 ul of MTBE for 1 hr at room temperature to separate organic-soluble lipids from aqueous-soluble lipids and other small-molecules. Finally, 360 ul of ultrapure water was added (for a final ratio of 3:1:0.9 MTBE:methanol:water) to resolve the two liquid phases, and each samples were centrifuged at 10,000 x g for 10 min. For this experiment, the upper organic phase was collected from each sample and stored in a separate tube, and the remaining protein pellets were resuspended in 25 mM ammonium bicarbonate, pH 8, with 2.5% SDS. A BCA protein assay was performed on each protein fraction, and the organic phase was normalized to their protein concentration equivalent with 100% methanol. All samples were then stored at -80°C prior to analysis. |
Combined analysis:
| Analysis ID | AN002951 | AN002952 | AN002953 |
|---|---|---|---|
| Analysis type | MS | MS | MS |
| Chromatography type | Reversed phase | Reversed phase | HILIC |
| Chromatography system | Agilent 1260 | Agilent 1260 | Agilent 1260 |
| Column | Agilent Eclipse XDB-C18 (100 x 3.0mm) | Agilent Eclipse XDB-C18 (100 x 3.0mm) | Phenomenex Luna NH2 (150 x 2.1mm,3um) |
| MS Type | ESI | ESI | ESI |
| MS instrument type | Triple quadrupole | Triple quadrupole | Triple quadrupole |
| MS instrument name | Agilent 6490 QQQ | Agilent 6490 QQQ | Agilent 6490 QQQ |
| Ion Mode | NEGATIVE | POSITIVE | POSITIVE |
| Units | area under the curve | area under the curve | area under the curve |
Chromatography:
| Chromatography ID: | CH002186 |
| Chromatography Summary: | Reverse phase negative mode |
| Instrument Name: | Agilent 1260 |
| Column Name: | Agilent Eclipse XDB-C18 (100 x 3.0mm) |
| Chromatography Type: | Reversed phase |
| Chromatography ID: | CH002187 |
| Chromatography Summary: | Normal phase |
| Instrument Name: | Agilent 1260 |
| Column Name: | Phenomenex Luna NH2 (150 x 2.1mm,3um) |
| Chromatography Type: | HILIC |
MS:
| MS ID: | MS002741 |
| Analysis ID: | AN002951 |
| Instrument Name: | Agilent 6490 QQQ |
| Instrument Type: | Triple quadrupole |
| MS Type: | ESI |
| MS Comments: | Lipid profiling was performed using an Agilent 1260 HPLC coupled to an Agilent 6490 triple quadrupole (QQQ) mass spectrometer (41). Each sample was run through three separate chromatographic conditions (reverse-phase negative mode, reverse-phase positive mode and normal-phase positive mode) for the effective quantification of 337 distinct lipids from 28 lipid subclasses, as previously described (41). Individual lipid species were measured by multiple reaction monitoring transitions. |
| Ion Mode: | NEGATIVE |
| MS ID: | MS002742 |
| Analysis ID: | AN002952 |
| Instrument Name: | Agilent 6490 QQQ |
| Instrument Type: | Triple quadrupole |
| MS Type: | ESI |
| MS Comments: | Lipid profiling was performed using an Agilent 1260 HPLC coupled to an Agilent 6490 triple quadrupole (QQQ) mass spectrometer (41). Each sample was run through three separate chromatographic conditions (reverse-phase negative mode, reverse-phase positive mode and normal-phase positive mode) for the effective quantification of 337 distinct lipids from 28 lipid subclasses, as previously described (41). Individual lipid species were measured by multiple reaction monitoring transitions. |
| Ion Mode: | POSITIVE |
| MS ID: | MS002743 |
| Analysis ID: | AN002953 |
| Instrument Name: | Agilent 6490 QQQ |
| Instrument Type: | Triple quadrupole |
| MS Type: | ESI |
| MS Comments: | Lipid profiling was performed using an Agilent 1260 HPLC coupled to an Agilent 6490 triple quadrupole (QQQ) mass spectrometer (41). Each sample was run through three separate chromatographic conditions (reverse-phase negative mode, reverse-phase positive mode and normal-phase positive mode) for the effective quantification of 337 distinct lipids from 28 lipid subclasses, as previously described (41). Individual lipid species were measured by multiple reaction monitoring transitions. |
| Ion Mode: | POSITIVE |
