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MB Sample ID: SA235211
| Local Sample ID: | H18 |
| Subject ID: | SU002431 |
| Subject Type: | Mammal |
| Subject Species: | Mus musculus |
| Taxonomy ID: | 10090 |
| Genotype Strain: | C57Bl/6 |
| Age Or Age Range: | 20 weeks (at euthanasia) |
| Gender: | Male and female |
| Animal Animal Supplier: | Jackson Labratories |
| Animal Light Cycle: | Standard light dark cycle |
| Animal Feed: | PicoLab Rodent Diet 20, 20% protein |
Select appropriate tab below to view additional metadata details:
Subject:
| Subject ID: | SU002431 |
| Subject Type: | Mammal |
| Subject Species: | Mus musculus |
| Taxonomy ID: | 10090 |
| Genotype Strain: | C57Bl/6 |
| Age Or Age Range: | 20 weeks (at euthanasia) |
| Gender: | Male and female |
| Animal Animal Supplier: | Jackson Labratories |
| Animal Light Cycle: | Standard light dark cycle |
| Animal Feed: | PicoLab Rodent Diet 20, 20% protein |
Factors:
| Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
|---|---|---|---|---|
| H18 | SA235211 | FL029180 | Female | Sex |
| H18 | SA235211 | FL029180 | Germ-Free | Microbiome Status |
Collection:
| Collection ID: | CO002424 |
| Collection Summary: | Samples were collected following mouse euthanasia. The humerus was obtained and bone marrow was flushed using PBS. Next, metabolites were extracted using methanol:acetone. |
| Sample Type: | Bone |
Treatment:
| Treatment ID: | TR002443 |
| Treatment Summary: | All C57Bl/6J mice (male, female, germ-free, conventional) were housed at Montana State University. During this time, mice were kept on a light/dark cycle and fed a standard chow diet ad libitum. Upon 20 weeks of age, mice were euthanized. No additional factors such as injury, diet, or exercise occurred. Mice were employed to analyze differences in bone at macro and micro levels that are associated with the microbiome and sex. |
Sample Preparation:
| Sampleprep ID: | SP002437 |
| Sampleprep Summary: | Once euthanized, tissues were dissected and harvested for various techniques. For metabolomics, humeri samples underwent homogenization/crushing, extracted with methanol:acetone, and were then subjected to rounds of vortexing and centrifugation. Once metabolites were isolated, samples were dried via vacuum concentration and resuspended with acetonitrile:water for LC-MS analysis. |
Combined analysis:
| Analysis ID | AN003826 |
|---|---|
| Analysis type | MS |
| Chromatography type | HILIC |
| Chromatography system | Agilent 1290 |
| Column | Cogent Diamond Hydride (150 × 2.1mm,4um) |
| MS Type | ESI |
| MS instrument type | Single quadrupole |
| MS instrument name | Agilent 6538 QTOF |
| Ion Mode | POSITIVE |
| Units | Peak Intensity |
Chromatography:
| Chromatography ID: | CH002831 |
| Chromatography Summary: | Samples were analyzed using an Agilent 1290 UPLC coupled to an Agilent 6538 QTOF. All samples were run in normal phase using a Cogent Diamond Hydride HILIC column (150 x 2.1 mm; 100Å pore size on a 4µm particle size). Solvents: 0.1% formic acid in water (A), 0.1% formic acid in acetonitrile (B). Elution gradient: 100 to 25% solvent B over 17 minutes, 0 to 70% solvent A over 20 minutes, at 21 minutes, B increases from 25% to 100% till 25 minutes while A decreases from 70% to 0% till 25 minutes. The last 4 minutes act as a wash. Total run time = 25 minute method (per sample) |
| Instrument Name: | Agilent 1290 |
| Column Name: | Cogent Diamond Hydride (150 × 2.1mm,4um) |
| Flow Gradient: | 100 to 25% solvent B over 17 minutes, 0 to 70% solvent A over 20 minutes, at 21 minutes, B increases from 25% to 100% till 25 minutes while A decreases from 70% to 0% till 25 minutes. The last 4 minutes act as a wash. |
| Flow Rate: | 0.400 mL/min |
| Injection Temperature: | 4C |
| Solvent A: | 100% water; 0.1% formic acid |
| Solvent B: | 100% acetonitrile; 0.1% formic acid |
| Analytical Time: | 25 minutes |
| Chromatography Type: | HILIC |
MS:
| MS ID: | MS003568 |
| Analysis ID: | AN003826 |
| Instrument Name: | Agilent 6538 QTOF |
| Instrument Type: | Single quadrupole |
| MS Type: | ESI |
| MS Comments: | Data was acquired in positive mode following a 25-minute method. Following injection and acquisition, .d files were converted to .mzMLs using MSConvert (Threshold peak filter value = 1000; Peak picking = true, 1-1; 32-bit, no z-lib compression). Once .mzMLs were avaiable, XCMS was used (parameters reflected run parameters = positive mode, feature detection 15 ppm, adducts = [M+H]+, [M+Na]+ |
| Ion Mode: | POSITIVE |
