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MB Sample ID: SA015967
| Local Sample ID: | Micro434 |
| Subject ID: | SU000380 |
| Subject Type: | mouse |
| Subject Species: | Mus musculus |
| Taxonomy ID: | 10090 |
| Genotype Strain: | C57Bl/6 |
| Age Or Age Range: | 5.5 mo |
| Weight Or Weight Range: | 29.1 g-49.2 g |
| Gender: | male |
| Animal Animal Supplier: | JAX |
| Animal Housing: | 4/cage |
| Animal Feed: | Purina chow |
| Species Group: | Mammal |
Select appropriate tab below to view additional metadata details:
Subject:
| Subject ID: | SU000380 |
| Subject Type: | mouse |
| Subject Species: | Mus musculus |
| Taxonomy ID: | 10090 |
| Genotype Strain: | C57Bl/6 |
| Age Or Age Range: | 5.5 mo |
| Weight Or Weight Range: | 29.1 g-49.2 g |
| Gender: | male |
| Animal Animal Supplier: | JAX |
| Animal Housing: | 4/cage |
| Animal Feed: | Purina chow |
| Species Group: | Mammal |
Factors:
| Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
|---|---|---|---|---|
| Micro434 | SA015967 | FL003486 | no | HSV-1 |
| Micro434 | SA015967 | FL003486 | LF | Diet at Week 2 |
Collection:
| Collection ID: | CO000374 |
| Collection Summary: | For extraction, 500 µL of an ice-cold solution of 90:10 Methanol:Chloroform (v/v) ¬was added to the tubes containing the thawed cell pellets. MagNA lyser ceramic beads were added to the tubes, and a MagNA lyser was used to beat the samples for two 30 seconds pulses at 2,000 rpm placing samples on cold block for 5 min in between pulses. Sonication for 5 min was performed to the beaten cell samples, followed by centrifugation at room temperature and at 16,000rcf for 4 min. A 350 µL aliquot of each experimental cell sample homogenized supernatant was transferred to a labeled 2.0 mL Lo-Bind Eppendorf tube |
| Sample Type: | brain homogenate |
Treatment:
| Treatment ID: | TR000394 |
| Treatment Summary: | 3-week old mice were placed on a 10% low fat (LF) diet and acclimated for one week prior to intranasal HSV-1 infection or mock infection with PBS. Fourteen days post-infection mice were randomized to either a 45% high fat diet (HF) or remained on the LF diet. Eight weeks post-diet transition, mice were euthanized and brain tissue samples were collected and processed for metabolomics. |
Sample Preparation:
| Sampleprep ID: | SP000387 |
| Sampleprep Summary: | For extraction, 500 µL of an ice-cold solution of 90:10 Methanol:Chloroform (v/v) ¬was added to the tubes containing the thawed cell pellets. MagNA lyser ceramic beads were added to the tubes, and a MagNA lyser was used to beat the samples for two 30 seconds pulses at 2,000 rpm placing samples on cold block for 5 min in between pulses. Sonication for 5 min was performed to the beaten cell samples, followed by centrifugation at room temperature and at 16,000rcf for 4 min. A 350 µL aliquot of each experimental cell sample homogenized supernatant was transferred to a labeled 2.0 mL Lo-Bind Eppendorf tube Analytical pooled samples were created by combining a 125 µL aliquot from each experimental sample in a labeled 20 mL glass vial. The QC pooled sample was vortexed for 30 sec and 350 µL aliquots were transferred to 5 labeled 2.0 mL Lo-Bind eppendorf tubes. Next, the supernatants of the study and QC pooled samples were dried overnight using a lyophilizer. The residue was reconstituted in 50 µL of reconstitution buffer (95:5 Water:Methanol, v/v) and mixed on an analog vortex mixer for 1 min with speed set at 10. Then, the samples were centrifuged at room temperature for 4 min at 16,000 rcf, and the supernatants were transferred to autosampler vials for data acquisition. |
Combined analysis:
| Analysis ID | AN000588 | AN000589 |
|---|---|---|
| Analysis type | MS | MS |
| Chromatography type | Reversed phase | Reversed phase |
| Chromatography system | Synapt G2 Si ESI-Q-TOF | Synapt G2 Si ESI-Q-TOF |
| Column | Waters ACQUITY UPLC HSS T3 | Waters ACQUITY UPLC HSS T3 |
| MS Type | ESI | ESI |
| MS instrument type | QTOF | QTOF |
| MS instrument name | Waters Synapt G2 Si QTOF | Waters Synapt G2 Si QTOF |
| Ion Mode | POSITIVE | NEGATIVE |
| Units | intensity | intensity |
Chromatography:
| Chromatography ID: | CH000422 |
| Chromatography Summary: | UPLC-MS spectra were collected for all samples. UPLC was performed on a Waters Acquity UPLC with an Acquity HSS T3 column (2.1x 100mm x 1.8 µm) at 50 °C using the reversed-phase separation. Water with 0.1% formic acid (mobile phase A) and methanol with 0.1% formic acid (mobile phase B) were used as mobile phases and the metabolites were chromatographically separated using a gradient separation: (see the 3. Sheridan-Mice-Microglia Cells_RP-Metadata and Analytical Metadata.xlsx file for the flow gradient). Mass spectroscopy analysis was performed using a Synapt G2 Si ESI-Q-TOF using a 10 µL injection volume. UPLC-MS data were collected over 70-1000 m/z in both positive and negative modes. |
| Methods Filename: | RTI-RCMRC-RP |
| Instrument Name: | Synapt G2 Si ESI-Q-TOF |
| Column Name: | Waters ACQUITY UPLC HSS T3 |
| Flow Rate: | .4ml/min |
| Injection Temperature: | 8 C |
| Solvent A: | 100% water; 0.1% formic acid |
| Solvent B: | 100% methanol; 0.1% formic acid |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS000524 |
| Analysis ID: | AN000588 |
| Instrument Name: | Waters Synapt G2 Si QTOF |
| Instrument Type: | QTOF |
| MS Type: | ESI |
| Ion Mode: | POSITIVE |
| Analysis Protocol File: | RTI-RCMRC-RP-POS |
| MS ID: | MS000525 |
| Analysis ID: | AN000589 |
| Instrument Name: | Waters Synapt G2 Si QTOF |
| Instrument Type: | QTOF |
| MS Type: | ESI |
| Ion Mode: | NEGATIVE |
| Analysis Protocol File: | RTI-RCMRC-RP-NEG |
