Return to study ST001819 main page
MB Sample ID: SA169077
Local Sample ID: | EC22 |
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 |
---|---|---|---|---|
EC22 | SA169077 | FL020173 | EC | Region |
EC22 | SA169077 | FL020173 | E4/4 | 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 |