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MB Sample ID: SA001683
| Local Sample ID: | LPL203 |
| Subject ID: | SU000050 |
| Subject Type: | Animal |
| Subject Species: | Mus musculus |
| Taxonomy ID: | 10090 |
| Genotype Strain: | NOD/ShiLtj |
| Gender: | Male |
| Animal Animal Supplier: | Jackson Laboratories |
| Animal Housing: | SPF (Helicobacter neg / MNV neg) |
| Animal Feed: | normal chow |
| Species Group: | Mammal |
Select appropriate tab below to view additional metadata details:
Subject:
| Subject ID: | SU000050 |
| Subject Type: | Animal |
| Subject Species: | Mus musculus |
| Taxonomy ID: | 10090 |
| Genotype Strain: | NOD/ShiLtj |
| Gender: | Male |
| Animal Animal Supplier: | Jackson Laboratories |
| Animal Housing: | SPF (Helicobacter neg / MNV neg) |
| Animal Feed: | normal chow |
| Species Group: | Mammal |
Factors:
| Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
|---|---|---|---|---|
| LPL203 | SA001683 | FL000568 | Pool QC | Treatment Group |
Collection:
| Collection ID: | CO000033 |
| Sample Type: | liver |
| Collection Time: | 6 weeks |
Treatment:
| Treatment ID: | TR000051 |
| Treatment Summary: | Three mice were exposed to PAT and 3 mice were non-exposed controls. PAT= therapeutic dose-pulsed antibiotic treatment. |
| Treatment Compound: | PAT |
Sample Preparation:
| Sampleprep ID: | SP000046 |
| Sampleprep Summary: | Frozen liver samples were weighed (50-100 mg) into labeled homogenizer bead tubes. Cold acetonitrile:water (50%) was added to tissue based on weight to make 1 mg/mL homogenates. The samples were extracted and homogenized on a Spex Geno/Grinder for two 45 second pulses at 1750 rpm. Samples were centrifuged at 12000 rcf for 5 min. Liver supernatants were transferred into BSI-labeled tubes. A 500 μL aliquot/sample was transferred into a second set of BSI-labeled tubes for further processing. To make pooled samples, a 300 μL aliquot of selected TranSTAT liver supernatants was combined in a 2 mL tube and used for QC samples in DuraSTAT, TranSTAT, EstroSTAT and NOD sub-studies. Additionally, a 200 μL aliquot of selected VG STAT liver supernatants was combined in a separate 2 mL tube and used as QC samples in the VG STAT sub-study. Three 500 μL aliquots were transferred into BSI-labeled tubes for each set of Pooled QC samples. All samples were then dried on an Eppendorf rotaVap (V-AL setting) at 30°C until dry and stored at -80 °C. On the second day of processing, 630 μL of D2O was added into each dried liver extract tube. 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), and the samples were vortexed on a multi-tube vortexer for 10 minutes at speed 5. Tubes were then centrifuged at 12000 rcf for 5 minutes and a 600 μL aliquot of the supernatant was transferred into 5mm NMR tubes (Wilmad LabGlass, New Jersey, USA) which were kept on ice until data acquisition. |
| Sampleprep Protocol Filename: | NOD_Liver_Metabolomics_Procedure.docx |
Chromatography:
| Chromatography ID: | CH000034 |
Analysis:
| MB Sample ID: | SA001683 |
| Analysis ID: | AN000053 |
| 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: | CH000034 |
| Num Factors: | 3 |
NMR:
| NMR ID: | NM000015 |
| Analysis ID: | AN000053 |
| 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: | 10 |
| Offset Frequency: | 3293 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 |
