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MB Sample ID: SA072517
| Local Sample ID: | SB5 |
| Subject ID: | SU001119 |
| Subject Type: | Mammal |
| Subject Species: | Rattus norvegicus |
| Taxonomy ID: | 10116 |
| Genotype Strain: | F344/Ntac-Apc-+/Pirc |
| Age Or Age Range: | 30 |
| Animal Animal Supplier: | Taconic and Envigo |
| Animal Housing: | Conventional, |
| Animal Feed: | Labdiet 5058 |
| Animal Water: | Autoclaved, purified with sulfuric acid |
Select appropriate tab below to view additional metadata details:
Subject:
| Subject ID: | SU001119 |
| Subject Type: | Mammal |
| Subject Species: | Rattus norvegicus |
| Taxonomy ID: | 10116 |
| Genotype Strain: | F344/Ntac-Apc-+/Pirc |
| Age Or Age Range: | 30 |
| Animal Animal Supplier: | Taconic and Envigo |
| Animal Housing: | Conventional, |
| Animal Feed: | Labdiet 5058 |
| Animal Water: | Autoclaved, purified with sulfuric acid |
Factors:
| Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
|---|---|---|---|---|
| SB5 | SA072517 | FL011375 | GM;LEW | Group |
Collection:
| Collection ID: | CO001113 |
| Collection Summary: | Fecal samples collected at 1 month of age, prior to any observable disease onset. F344 refers to Fisher (F344) rats, whereas as GM:SD refers to the GM from Sprague-Dawley rats, while GM:LEW refers to the gut microbiota (GM) from Lewis rats |
| Collection Protocol ID: | 8732 |
| Sample Type: | Feces |
| Collection Method: | Sterile, asceptic method. Animals were placed in clean, sterile cages and feces were speared with sterile, autoclaved toothpicks. |
| Collection Location: | Discovery Ridge, Columbia MO |
| Storage Conditions: | -80℃ |
| Collection Vials: | Glass |
| Storage Vials: | Glass |
Treatment:
| Treatment ID: | TR001133 |
| Treatment Summary: | Pirc rats were rederived using 3 surrogate dams, each with distinct gut microbiota profiles |
| Treatment Protocol ID: | 8732 |
Sample Preparation:
| Sampleprep ID: | SP001126 |
| Sampleprep Summary: | Fecal samples were lyophilized at -20 ˚C using 0.1 millibar of vacuum pressure, following which dried samples (30 mg) were extracted sequentially for both UHPLC-MS and GC-MS. The dried samples were first treated with 1.0 mL of 80% MeOH containing 18 µg/mL umbelliferone, sonicated for 5 minutes and centrifuged for 40 minutes at 3000 g at 10 ºC. 0.5 mL of supernatant was used for UHPLC-MS analysis after a subsequent spin at 5000 g at 10 ºC for 20 minutes and transferring 250 µL of the sample into glass autosampler vials with inserts. For GC-MS (Gas Chromatography-Mass Spectrometry) analyses of primary polar metabolites, 0.5 mL water was added the remaining extract used above for the UHPLC preparation, sonicated for 5 min, extracted for 30min, and centrifuged at 3000 g. 0.5 mL of the polar extract was subsequently dried under nitrogen and derivatized using previously established protocols (84). Briefly, N-Methyl-N-(trimethylsilyl) trifluoroacetamide (MSTFA) with 1 % TMCS (2,2,2-Trifluoro-N-methyl-N-(trimethylsilyl)-acetamide, Chlorotrimethylsilane) was used to derivatize the polar metabolites, after treatment with methoxyamine-HCl-pyridine. |
Combined analysis:
| Analysis ID | AN001757 |
|---|---|
| Analysis type | MS |
| Chromatography type | Reversed phase |
| Chromatography system | Agilent 1290 |
| Column | Waters Acquity BEH C18 (150 x 2.1mm,1.7um) |
| MS Type | ESI |
| MS instrument type | QTOF |
| MS instrument name | Bruker maXis Impact qTOF |
| Ion Mode | NEGATIVE |
| Units | Peak Area |
Chromatography:
| Chromatography ID: | CH001241 |
| Instrument Name: | Agilent 1290 |
| Column Name: | Waters Acquity BEH C18 (150 x 2.1mm,1.7um) |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS001625 |
| Analysis ID: | AN001757 |
| Instrument Name: | Bruker maXis Impact qTOF |
| Instrument Type: | QTOF |
| MS Type: | ESI |
| Ion Mode: | NEGATIVE |
