Return to study ST000029 main page
MB Sample ID: SA001636
| Local Sample ID: | CPL101 |
| Subject ID: | SU000046 |
| Subject Type: | Animal |
| Subject Species: | Mus musculus |
| Taxonomy ID: | 10090 |
| Genotype Strain: | Swiss Webster Mice |
| Gender: | Female |
| Animal Animal Supplier: | Taconic |
| Animal Housing: | Conventional |
| Animal Feed: | High Fat Diet |
| Species Group: | Mammal |
Select appropriate tab below to view additional metadata details:
Subject:
| Subject ID: | SU000046 |
| Subject Type: | Animal |
| Subject Species: | Mus musculus |
| Taxonomy ID: | 10090 |
| Genotype Strain: | Swiss Webster Mice |
| Gender: | Female |
| Animal Animal Supplier: | Taconic |
| Animal Housing: | Conventional |
| Animal Feed: | High Fat Diet |
| Species Group: | Mammal |
Factors:
| Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
|---|---|---|---|---|
| CPL101 | SA001636 | FL000555 | Pooled QC | Treatment Group |
Collection:
| Collection ID: | CO000029 |
| Collection Summary: | - |
| Sample Type: | cecal contents |
| Collection Time: | 8 weeks |
Treatment:
| Treatment ID: | TR000047 |
| Treatment Summary: | Three mice were inoculated with cecal contents from STAT mice and 3 mice were inoculated with cecal contents from control mice. STAT = sub-therapeutic antibiotic treatment. |
| Treatment Route: | cecal transfer |
Sample Preparation:
| Sampleprep ID: | SP000042 |
| Sampleprep Summary: | Frozen cecal contents (cecal) samples were weighed into labeled homogenizer bead tubes. D20 was added to each tube (500 µL if less than 50 mg and 1000 µL if more than 100 mg of tissue). The samples were homogenized on a Spex Geno/Grinder for two 30 second pulses at 1750 rpm. Samples were centrifuged at 12000 rcf for 5 min. Cecal supernatants were transferred (450/700 µL) into 2.0 mL 0.2 µm nylon filter tubes and centrifuged at 16000 rcf until all the homogenate was filtered. The 200 µL remaining aliquot from each 1000 µL cecal sample was combined in a 10 mL tube and vortexed for 30 seconds to generate pooled samples for QC during analysis. Three “low” QC pools were generated by transferring 450 µL of the pooled homogenate into 2.0 mL 0.2 µm nylon filter tubes; and three “high” QC pools were generated by transferring 700 µL of the pooled homogenate into 2.0 mL 0.2 µm nylon filter tubes and also centrifuged at 16000 rcf until all the homogenate was filtered. The volume of homogenate needed to analyze 50 mg/sample and volume of D20 needed to bring the total volume to 630 µL was calculated. The calculated volumes of filtered supernatant and D20 were then transferred into BSI-labeled tubes. Chenomx Internal Standard solution (Chenomx ISTD, Edmonton, Alberta, Canada) contains 5mM 4,4-dimethyl-4-silapentane-1-sulfonic acid (DSS, Chemical Shift Indicator), 100 mM Imidazole (pH indicator), and 0.2% NaN3 (to inhibit bacterial growth) was added (70 µl) to the tubes. Samples were vortexed for 30 seconds and centrifuged at 12000 rcf for 5 minutes. A 600 µL aliquot of the supernatant was then transferred into 5mm NMR tubes (Wilmad LabGlass, New Jersey, USA) which were kept on ice until data acquisition. |
| Sampleprep Protocol Filename: | TranSTAT_Cecal_Metabolomics_Procedure.docx |
Analysis:
| MB Sample ID: | SA001636 |
| Analysis ID: | AN000049 |
| Laboratory Name: | RTI/ DHHMRI |
| Analysis Type: | NMR |
| Analysis Comments: | NMR (700 MHz) |
| Acquisition Date: | 41527 |
| Software Version: | Top Spin 3.2 |
| Operator Name: | Wimal Pathmasiri/ Kevin Knagge/ Jason Winnikie |
| Randomization Order: | yes |
| Detector Type: | NMR |
| Data Format: | NMR |
| Chromatography ID: | CH000030 |
| Num Factors: | 3 |
NMR:
| NMR ID: | NM000011 |
| Analysis ID: | AN000049 |
| Instrument Name: | Bruker Avance III |
| Instrument Type: | FT-NMR |
| NMR Experiment Type: | 1D 1H |
| Field Frequency Lock: | Deuterium |
| Standard Concentration: | 0.5mM |
| Spectrometer Frequency: | 700 MHz |
| NMR Probe: | cyrogenically cooled ATMA inverse probe |
| NMR Solvent: | D2O |
| NMR Tube Size: | 5mm x 4inch |
| Shimming Method: | topshim |
| Pulse Sequence: | noesypr1d |
| Water Suppression: | presat |
| Pulse Width: | 14.84 us |
| Power Level: | 25.704w |
| Receiver Gain: | 9 |
| Offset Frequency: | 3296 Hz |
| Chemical Shift Ref Cpd: | DSS |
| Temperature: | 298.1 K |
| Number Of Scans: | 64 |
| Dummy Scans: | 4 |
| Acquisition Time: | 2.3243434 |
| Relaxation Delay: | 2 s |
| Spectral Width: | 20.1358 |
| Num Data Points Acquired: | 65536 |
| Real Data Points: | 65536 |
| Line Broadening: | 0.5 |
| Zero Filling: | yes |
| Apodization: | lorentzian |
| Baseline Correction Method: | polynomial |
| Chemical Shift Ref Std: | DSS |
