Return to study ST001247 main page
MB Sample ID: SA090866
Local Sample ID: | 3WK_placebo_35_026 |
Subject ID: | SU001315 |
Subject Type: | Mammal |
Subject Species: | Canis lupus familiaris |
Taxonomy ID: | 9615 |
Select appropriate tab below to view additional metadata details:
Subject:
Subject ID: | SU001315 |
Subject Type: | Mammal |
Subject Species: | Canis lupus familiaris |
Taxonomy ID: | 9615 |
Factors:
Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
---|---|---|---|---|
3WK_placebo_35_026 | SA090866 | FL013097 | 3WK | Time point |
3WK_placebo_35_026 | SA090866 | FL013097 | IBD | Status |
3WK_placebo_35_026 | SA090866 | FL013097 | prednisone | Treatment |
Collection:
Collection ID: | CO001309 |
Collection Summary: | Stool samples were collected from all dogs before initiating therapy with prednisone, after 3 and 8 weeks, and more than one year after beginning treatment. Thirteen healthy dogs were enrolled in the study as a control group. Stool samples were kept frozen at -80oC until DNA extraction. |
Sample Type: | Feces |
Storage Conditions: | -80℃ |
Treatment:
Treatment ID: | TR001330 |
Treatment Summary: | Thirteen dogs diagnosed with idiopathic IBD, that previously failed to respond to treatment with elimination diets and metronidazole, were enrolled. All dogs were treated with prednisone for 8 weeks. Healthy dogs enrolled as controls did not receive any treatment. |
Sample Preparation:
Sampleprep ID: | SP001323 |
Sampleprep Summary: | Fecal samples were lyophilized and approximately 10 mg was sent to the West Coast Metabolomics Center (WCMC) at University of California at Davis (http://metabolomics.ucdavis.edu/). Samples were analyzed on a gas chromatography time-of-flight mass spectrometry (GC–TOF–MS) platform, in accordance with published methods. Briefly, samples underwent homogenization and extraction, followed by centrifugation. Dried supernatant was resuspended in methanol/chloroform and internal standards were added, followed by drying and derivatization by methoxyamine hydrochloride and N-methyl-N-trimethylsilyltrifluoroacetamide. A volume of 0.5 μL was injected in splitless mode onto a Restek rtx5SilMS column on a temperature-gradient programmed GC (oven 50–330 °C at 20 °C/min, injector 50–250 °C at 12 °C/ sec) coupled with a Leco Pegasus IV mass spectrometer (scanning 70 spectra/sec from 80 to 500 Da, −70 eV ionization energy, 1800 V detector voltage) with helium carrier gas (1 mL/min). Raw data files were processed using ChromaTOF v. 2.32. BinBase algorithm matched spectra to database compounds, and quantification was reported by peak height of an ion at the specific retention index characteristic of the compound across all samples. Peak heights were normalized by average total peak-sums for identified compounds across each sample group. |
Combined analysis:
Analysis ID | AN002071 |
---|---|
Analysis type | MS |
Chromatography type | GC |
Chromatography system | Agilent 6890N |
Column | Restek Rtx-5Sil (30m x 0.25mm,0.25um) |
MS Type | EI |
MS instrument type | GC-TOF |
MS instrument name | Leco Pegasus IV TOF |
Ion Mode | POSITIVE |
Units | peak area |
Chromatography:
Chromatography ID: | CH001508 |
Instrument Name: | Agilent 6890N |
Column Name: | Restek Rtx-5Sil (30m x 0.25mm,0.25um) |
Chromatography Type: | GC |
MS:
MS ID: | MS001922 |
Analysis ID: | AN002071 |
Instrument Name: | Leco Pegasus IV TOF |
Instrument Type: | GC-TOF |
MS Type: | EI |
MS Comments: | Raw data files are preprocessed directly after data acquisition and stored as ChromaTOF-specific *.peg files, as generic *.txt result files and additionally as generic ANDI MS *.cdf files. ChromaTOF vs. 2.32 is used for data preprocessing without smoothing, 3 s peak width, baseline subtraction just above the noise level, and automatic mass spectral deconvolution and peak detection at signal/noise levels of 5:1 throughout the chromatogram. Apex masses are reported for use in the BinBase algorithm. Result *.txt files are exported to a data server with absolute spectra intensities and further processed by a filtering algorithm implemented in the metabolomics BinBase database. |
Ion Mode: | POSITIVE |