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MB Sample ID: SA171992
| Local Sample ID: | S18 |
| Subject ID: | SU001925 |
| Subject Type: | Mammal |
| Subject Species: | Mus musculus |
| Taxonomy ID: | 10090 |
| Genotype Strain: | APPSwe/PS1ΔE9 (APP/PSEN1) |
| Age Or Age Range: | 12 month |
| Gender: | Male and female |
Select appropriate tab below to view additional metadata details:
Subject:
| Subject ID: | SU001925 |
| Subject Type: | Mammal |
| Subject Species: | Mus musculus |
| Taxonomy ID: | 10090 |
| Genotype Strain: | APPSwe/PS1ΔE9 (APP/PSEN1) |
| Age Or Age Range: | 12 month |
| Gender: | Male and female |
Factors:
| Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
|---|---|---|---|---|
| S18 | SA171992 | FL020667 | M | gender |
| S18 | SA171992 | FL020667 | APP | genotype |
| S18 | SA171992 | FL020667 | REV | treatment |
Collection:
| Collection ID: | CO001918 |
| Collection Summary: | Liver samples from male and female APPSwe/PS1ΔE9 (APP/PSEN1) transgenic mice and wild-type (WT) littermates were collected after sacrifice at 12 months. These mice are a subset of mice for which behavioral and biochemical data have already been published, including weight change and diabetic state as assessed by glucose tolerance tests.After sacrifice, liver tissue samples were taken and put immediately on dry ice and stored at −80°C until used in the analytical workflow described herein. |
| Sample Type: | Liver |
| Storage Conditions: | -80℃ |
Treatment:
| Treatment ID: | TR001937 |
| Treatment Summary: | Briefly, at 2-months of age, standard lab chow (Purina 5001, 4% kcal/fat) was replaced with either HFD in which 60% kcal are derived from lard, 20% from carbohydrate and 20% from protein, or low-fat diet (LFD) control in which 10% kcal are derived from lard and additional calories are derived from corn starch, with 70% from carbohydrates and 20% from protein.33 For the reversal group (REV), a subset of mice on the HFD was provided with a LFD, at 9.5 months of age, for the study duration.33 All other mice were maintained on their original experimental diets until the end of the study, which was an additional 10 weeks. |
Sample Preparation:
| Sampleprep ID: | SP001931 |
| Sampleprep Summary: | For liver samples, frozen tissues were first individually pulverized using a mortar and pestle followed by lysing in 1 mL ice-cold lysis buffer ((1:1:2, ACN:MeOH:ammonium bicarbonate (0.1 M, pH 8.0) (LC-MS grade)). Individual samples were sonicated using a probe tip sonicator, 10 pulses, at 30% power, and cooled on ice between samples. A bicinchoninic acid (BCA) protein assay was used to determine the protein concentration for each individual sample and adjusted to a total amount of protein of 200 µg. For untargeted MS studies, SIL-ISs biotin-D2 and phenylalanine-D8 were added to each sample to assess sample processing steps (metabolite extraction and reconstitution). Following lysis and addition of SIL-ISs, protein precipitation was performed by adding 800 µL of ice-cold methanol (4x by volume). Samples were incubated at -80°C overnight. Following incubation, samples were centrifuged at 10,000 rpm for 10 min. The supernatant containing metabolites were dried in vacuo and metabolite extracts were stored frozen at -80 °C until ready to use. |
| Processing Storage Conditions: | -80℃ |
| Extraction Method: | Following lysis and standard addition, protein precipitation was performed by adding 800µL of ice-cold methanol (4x by volume). Samples were incubated at -80°C overnight. Following incubation, samples were centrifuged at 10,000 rpm for 10 min to eliminate proteins. The supernatants containing metabolites were dried via speed-vacuum. |
| Extract Storage: | -80℃ |
Combined analysis:
| Analysis ID | AN002992 |
|---|---|
| Analysis type | MS |
| Chromatography type | Reversed phase |
| Chromatography system | Thermo Vanquish |
| Column | Thermo Hypersil Gold (100 x 2. mm,1.9um) |
| MS Type | ESI |
| MS instrument type | Orbitrap |
| MS instrument name | Thermo Q Exactive Orbitrap |
| Ion Mode | POSITIVE |
| Units | time_m/z |
Chromatography:
| Chromatography ID: | CH002219 |
| Instrument Name: | Thermo Vanquish |
| Column Name: | Thermo Hypersil Gold (100 x 2. mm,1.9um) |
| Column Temperature: | 40 |
| Flow Gradient: | 0.250 |
| Flow Rate: | 0.25 mL/min |
| Injection Temperature: | 8 |
| Sample Injection: | 5 |
| Solvent A: | 100% water; 0.1% formic acid |
| Solvent B: | 100% acetonitrile, 0.1% formic acid |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS002781 |
| Analysis ID: | AN002992 |
| Instrument Name: | Thermo Q Exactive Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | XCalibur software for data acquisition Progenesis QI 2.0 for data processing |
| Ion Mode: | POSITIVE |
