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MB Sample ID: SA169229
| Local Sample ID: | 25 |
| Subject ID: | SU001900 |
| Subject Type: | Mammal |
| Subject Species: | Equus caballus |
| Taxonomy ID: | 9796 |
Select appropriate tab below to view additional metadata details:
Subject:
| Subject ID: | SU001900 |
| Subject Type: | Mammal |
| Subject Species: | Equus caballus |
| Taxonomy ID: | 9796 |
Factors:
| Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
|---|---|---|---|---|
| 25 | SA169229 | FL020192 | CON | Group |
Collection:
| Collection ID: | CO001893 |
| Collection Summary: | Fecal samples were collected from horses that were matched for diet and antimicrobial agent (including dose, route and duration of therapy). |
| Collection Protocol Filename: | Collection_protocol.docx |
| Sample Type: | Feces |
| Storage Conditions: | -80℃ |
Treatment:
| Treatment ID: | TR001913 |
| Treatment Summary: | Horses were prescribed antimicrobials as prophylaxis before elective surgery (excluding surgery of the gastrointestinal tract including colic) or to treat a suspected or confirmed infection. |
Sample Preparation:
| Sampleprep ID: | SP001906 |
| Sampleprep Summary: | Five-hundred mg of feces was aliquoted into a 2ml tube, lyophilized overnight and vortexed with a 5mm stainless steel bead (Quiagen, Germantown, MD ) for 5 minutes. Samples were then extracted using a methanol:chloroform:water-based extraction method. Briefly 800 uL ice cold methanol:chloroform (1:1, v:v) was added to samples in a bead-based lysis tube (Bertin, Rockville, MD). Samples were homogenized for 30 seconds on a Precyllys 24 (Bertin, Rockville, MD) at a speed of 6000. The supernatant was collected and samples were homogenized a second time with 800 uL ice methanol:chloroform. 600 uL ice cold water was added to the combined extract, vortexed and centrifuged to separate the phases. The upper aqueous layer was passed through a 0.2 um nylon filter (Merck Millipore, Burlington, MA). 500 uL of the filtered aqueous phase was then passed through a 3 kDa cutoff column (Thermo Scientific, Waltham, MA) and the flow through was collected for analysis. |
Combined analysis:
| Analysis ID | AN002959 |
|---|---|
| Analysis type | MS |
| Chromatography type | Reversed phase |
| Chromatography system | Thermo Xcalibur |
| Column | Phenomenex Synergi Fusion (150mm x 2mm,4um) |
| MS Type | ESI |
| MS instrument type | Orbitrap |
| MS instrument name | Thermo Q Exactive Plus Orbitrap |
| Ion Mode | POSITIVE |
| Units | peak intensity |
Chromatography:
| Chromatography ID: | CH002192 |
| Chromatography Summary: | Samples were maintained at 4 °C before injection. The injection volume was 10 µL. Chromatographic separation was achieved on a Synergi Fusion 4µm, 150 mm x 2 mm reverse phase column (Phenomenex, Torrance, CA) maintained at 30 °C using a solvent gradient method. Solvent A was water (0.1% formic acid). Solvent B was methanol (0.1% formic acid). The gradient method used was 0-5 min (10% B to 40% B), 5-7 min (40% B to 95% B), 7-9 min (95% B), 9-9.1 min (95% B to 10% B), 9.1-13 min (10% B). The flow rate was 0.4 mL min-1. |
| Instrument Name: | Thermo Xcalibur |
| Column Name: | Phenomenex Synergi Fusion (150mm x 2mm,4um) |
| Column Temperature: | 30 |
| Flow Gradient: | 0-5 min (10% B to 40% B), 5-7 min (40% B to 95% B), 7-9 min (95% B), 9-9.1 min (95% B to 10% B), 9.1-13 min (10% B). |
| Flow Rate: | 0.4 mL/min |
| Solvent A: | 100% water; 0.1% formic acid |
| Solvent B: | 100% methanol; 0.1% formic acid |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS002749 |
| Analysis ID: | AN002959 |
| Instrument Name: | Thermo Q Exactive Plus Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | Sample acquisition was performed Xcalibur (Thermo Scientific). |
| Ion Mode: | POSITIVE |
| Analysis Protocol File: | MS_protocol.docx |
