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MB Sample ID: SA097560
| Local Sample ID: | Cecal content_GF1 |
| Subject ID: | SU001412 |
| Subject Type: | Mammal |
| Subject Species: | Mus musculus |
| Taxonomy ID: | 10090 |
Select appropriate tab below to view additional metadata details:
Subject:
| Subject ID: | SU001412 |
| Subject Type: | Mammal |
| Subject Species: | Mus musculus |
| Taxonomy ID: | 10090 |
Factors:
| Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
|---|---|---|---|---|
| Cecal content_GF1 | SA097560 | FL013657 | germ-free | Genotype |
Collection:
| Collection ID: | CO001407 |
| Collection Summary: | C57BL/6J wild type mice were originally purchased from Jackson Laboratories (Bar Harbor, MN, USA). Germ-free (GF) C57BL/6J mice were from the Pennsylvania State University Gnotobiotic Animal Research Facility. Mice were bred in-house and fed on a standard animal chow diet. Animal experiments were performed after approval by the Institutional Animal Care and Use Committee. Fresh cecal contents from conventional and GF mice were collected and stored at -80 °C. |
| Sample Type: | Cecum |
Treatment:
| Treatment ID: | TR001427 |
| Treatment Summary: | C57BL/6J wild type mice were originally purchased from Jackson Laboratories (Bar Harbor, MN, USA). Germ-free (GF) C57BL/6J mice were from the Pennsylvania State University Gnotobiotic Animal Research Facility. Mice were bred in-house and fed on a standard animal chow diet. Animal experiments were performed after approval by the Institutional Animal Care and Use Committee. Fresh cecal contents from conventional and GF mice were collected and stored at -80 °C. |
Sample Preparation:
| Sampleprep ID: | SP001420 |
| Sampleprep Summary: | Each mixture was homogenized with 1 mm zirconium beads using a BeadBlasterTM 24 (Benchmark Scientific, Edison, NJ, USA) homogenizer. All samples were homogenized according to the program parameters: 6500 - 1×30 - 005 (×3). After vortexing, samples were sonicated for 20 min in an ice water bath, prior to centrifugation at 20,000 × g for 20 min at 4 ℃. The supernatants were collected, dried in a Savant SpeedVac (Thermo Scientific, Waltham, MA, USA), and reconstituted in 100 μL of 3% methanol (v/v) containing 1 µM chlorpropamide (internal standard). |
| Sampleprep Protocol Filename: | MS_protocol_for_global_profiling.pdf |
Combined analysis:
| Analysis ID | AN002232 |
|---|---|
| Analysis type | MS |
| Chromatography type | Reversed phase |
| Chromatography system | Thermo Vanquish |
| Column | Waters Acquity BEH C18 (100 x 2mm,1.7um) |
| MS Type | ESI |
| MS instrument type | Orbitrap |
| MS instrument name | Thermo Fusion Tribrid Orbitrap |
| Ion Mode | POSITIVE |
| Units | peak area |
Chromatography:
| Chromatography ID: | CH001638 |
| Instrument Name: | Thermo Vanquish |
| Column Name: | Waters Acquity BEH C18 (100 x 2mm,1.7um) |
| Flow Gradient: | The initial condition was 97% A and 3% B, increasing to 45% B at 10 min and 75% B at 12 min, where it was held at 75% B until 17.5 min before returning to the initial conditions. |
| Solvent A: | 100% water; 0.1% formic acid; |
| Solvent B: | 100% acetonitrile; 0.1% formic acid |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS002078 |
| Analysis ID: | AN002232 |
| Instrument Name: | Thermo Fusion Tribrid Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | Solvent A was HPLC-grade water with 0.1% formic acid, and solvent B was HPLC-grade acetonitrile with 0.1% formic acid. The initial condition was 97% A and 3% B, increasing to 45% B at 10 min and 75% B at 12 min, where it was held at 75% B until 17.5 min before returning to the initial conditions. Differential analyses were performed by the use of Compound Discoverer (Thermo Fisher Scientific, Waltham, MA, USA) |
| Ion Mode: | POSITIVE |
