#METABOLOMICS WORKBENCH rachelpilla_20190903_172556 DATATRACK_ID:1812 STUDY_ID:ST001247 ANALYSIS_ID:AN002071 PROJECT_ID:PR000834 VERSION 1 CREATED_ON September 9, 2019, 1:15 pm #PROJECT PR:PROJECT_TITLE Longitudinal Characterization of the Fecal Metabolome in Dogs with Idiopathic PR:PROJECT_TITLE Inflammatory Bowel Disease PR:PROJECT_SUMMARY Thirteen dogs diagnosed with idiopathic IBD, that previously failed to respond PR:PROJECT_SUMMARY to treatment with elimination diets and metronidazole, were enrolled. Stool PR:PROJECT_SUMMARY samples were collected from all dogs before initiating therapy with prednisone, PR:PROJECT_SUMMARY after 3 and 8 weeks, and more than one year after beginning treatment. Thirteen PR:PROJECT_SUMMARY healthy dogs were enrolled in the study as a control group. PR:INSTITUTE Texas A&M PR:DEPARTMENT Department of Small Animal Clinical Sciences PR:LABORATORY Gastrointestinal Laboratory PR:LAST_NAME Pilla PR:FIRST_NAME Rachel PR:ADDRESS 4474 TAMU PR:EMAIL rpilla@cvm.tamu.edu PR:PHONE 9798622861 #STUDY ST:STUDY_TITLE Longitudinal Characterization of the Fecal Metabolome in Dogs with Idiopathic ST:STUDY_TITLE Inflammatory Bowel Disease ST:STUDY_SUMMARY Thirteen dogs diagnosed with idiopathic IBD, that previously failed to respond ST:STUDY_SUMMARY to treatment with elimination diets and metronidazole, were enrolled. Stool ST:STUDY_SUMMARY samples were collected from all dogs before initiating therapy with prednisone, ST:STUDY_SUMMARY after 3 and 8 weeks, and more than one year after beginning treatment. Thirteen ST:STUDY_SUMMARY healthy dogs were enrolled in the study as a control group. ST:INSTITUTE Texas A&M ST:DEPARTMENT Department of Small Animal Clinical Sciences ST:LABORATORY Gastrointestinal Laboratory ST:LAST_NAME Pilla ST:FIRST_NAME Rachel ST:ADDRESS 4474 TAMU ST:EMAIL rpilla@cvm.tamu.edu ST:PHONE 9798622861 #SUBJECT SU:SUBJECT_TYPE Other SU:SUBJECT_SPECIES Canis lupus familiaris SU:TAXONOMY_ID 9615 #SUBJECT_SAMPLE_FACTORS: SUBJECT(optional)[tab]SAMPLE[tab]FACTORS(NAME:VALUE pairs separated by |)[tab]Additional sample data SUBJECT_SAMPLE_FACTORS - BL_placebo_04_001 Time point:0WK | Status:IBD | Treatment:none SUBJECT_SAMPLE_FACTORS - BL_placebo_07_002 Time point:0WK | Status:IBD | Treatment:none SUBJECT_SAMPLE_FACTORS - BL_placebo_11_003 Time point:0WK | Status:IBD | Treatment:none SUBJECT_SAMPLE_FACTORS - BL_placebo_14_004 Time point:0WK | Status:IBD | Treatment:none SUBJECT_SAMPLE_FACTORS - BL_placebo_19_005 Time point:0WK | Status:IBD | Treatment:none SUBJECT_SAMPLE_FACTORS - BL_placebo_20_006 Time point:0WK | Status:IBD | Treatment:none SUBJECT_SAMPLE_FACTORS - BL_placebo_23_007 Time point:0WK | Status:IBD | Treatment:none SUBJECT_SAMPLE_FACTORS - BL_placebo_28_008 Time point:0WK | Status:IBD | Treatment:none SUBJECT_SAMPLE_FACTORS - BL_placebo_35_009 Time point:0WK | Status:IBD | Treatment:none SUBJECT_SAMPLE_FACTORS - 3WK_placebo_04_018 Time point:3WK | Status:IBD | Treatment:prednisone SUBJECT_SAMPLE_FACTORS - 3WK_placebo_07_019 Time point:3WK | Status:IBD | Treatment:prednisone SUBJECT_SAMPLE_FACTORS - 3WK_placebo_11_020 Time point:3WK | Status:IBD | Treatment:prednisone SUBJECT_SAMPLE_FACTORS - 3WK_placebo_14_021 Time point:3WK | Status:IBD | Treatment:prednisone SUBJECT_SAMPLE_FACTORS - 3WK_placebo_19_022 Time point:3WK | Status:IBD | Treatment:prednisone SUBJECT_SAMPLE_FACTORS - 3WK_placebo_20_023 Time point:3WK | Status:IBD | Treatment:prednisone SUBJECT_SAMPLE_FACTORS - 3WK_placebo_23_024 Time point:3WK | Status:IBD | Treatment:prednisone SUBJECT_SAMPLE_FACTORS - 3WK_placebo_28_025 Time point:3WK | Status:IBD | Treatment:prednisone SUBJECT_SAMPLE_FACTORS - 3WK_placebo_35_026 Time point:3WK | Status:IBD | Treatment:prednisone SUBJECT_SAMPLE_FACTORS - 8WK_placebo_04_035 Time point:8WK | Status:IBD | Treatment:prednisone SUBJECT_SAMPLE_FACTORS - 8WK_placebo_07_036 Time point:8WK | Status:IBD | Treatment:prednisone SUBJECT_SAMPLE_FACTORS - 8WK_placebo_11_037 Time point:8WK | Status:IBD | Treatment:prednisone SUBJECT_SAMPLE_FACTORS - 8WK_placebo_14_038 Time point:8WK | Status:IBD | Treatment:prednisone SUBJECT_SAMPLE_FACTORS - 8WK_placebo_19_039 Time point:8WK | Status:IBD | Treatment:prednisone SUBJECT_SAMPLE_FACTORS - 8WK_placebo_20_040 Time point:8WK | Status:IBD | Treatment:prednisone SUBJECT_SAMPLE_FACTORS - 8WK_placebo_23_041 Time point:8WK | Status:IBD | Treatment:prednisone SUBJECT_SAMPLE_FACTORS - 8WK_placebo_28_042 Time point:8WK | Status:IBD | Treatment:prednisone SUBJECT_SAMPLE_FACTORS - 8WK_placebo_35_043 Time point:8WK | Status:IBD | Treatment:prednisone SUBJECT_SAMPLE_FACTORS - LT_placebo_11_052 Time point:1YR | Status:IBD | Treatment:none SUBJECT_SAMPLE_FACTORS - LT_placebo_14_053 Time point:1YR | Status:IBD | Treatment:none SUBJECT_SAMPLE_FACTORS - LT_placebo_19_054 Time point:1YR | Status:IBD | Treatment:none SUBJECT_SAMPLE_FACTORS - LT_placebo_23_055 Time point:1YR | Status:IBD | Treatment:none SUBJECT_SAMPLE_FACTORS - LT_placebo_28_056 Time point:1YR | Status:IBD | Treatment:none SUBJECT_SAMPLE_FACTORS - Healthy_01_064 Time point:0WK | Status:HC | Treatment:none SUBJECT_SAMPLE_FACTORS - Healthy_02_065 Time point:0WK | Status:HC | Treatment:none SUBJECT_SAMPLE_FACTORS - Healthy_04_066 Time point:0WK | Status:HC | Treatment:none SUBJECT_SAMPLE_FACTORS - Healthy_05_067 Time point:0WK | Status:HC | Treatment:none SUBJECT_SAMPLE_FACTORS - Healthy_06_068 Time point:0WK | Status:HC | Treatment:none SUBJECT_SAMPLE_FACTORS - Healthy_07_069 Time point:0WK | Status:HC | Treatment:none SUBJECT_SAMPLE_FACTORS - Healthy_12_070 Time point:0WK | Status:HC | Treatment:none SUBJECT_SAMPLE_FACTORS - Healthy_18_071 Time point:0WK | Status:HC | Treatment:none SUBJECT_SAMPLE_FACTORS - Healthy_19_072 Time point:0WK | Status:HC | Treatment:none SUBJECT_SAMPLE_FACTORS - Healthy_20_073 Time point:0WK | Status:HC | Treatment:none SUBJECT_SAMPLE_FACTORS - Healthy_22_074 Time point:0WK | Status:HC | Treatment:none SUBJECT_SAMPLE_FACTORS - Healthy_23_075 Time point:0WK | Status:HC | Treatment:none SUBJECT_SAMPLE_FACTORS - Healthy_25_076 Time point:0WK | Status:HC | Treatment:none #COLLECTION CO:COLLECTION_SUMMARY Stool samples were collected from all dogs before initiating therapy with CO:COLLECTION_SUMMARY prednisone, after 3 and 8 weeks, and more than one year after beginning CO:COLLECTION_SUMMARY treatment. Thirteen healthy dogs were enrolled in the study as a control group. CO:COLLECTION_SUMMARY Stool samples were kept frozen at -80oC until DNA extraction. CO:SAMPLE_TYPE Feces CO:STORAGE_CONDITIONS -80℃ #TREATMENT TR:TREATMENT_SUMMARY Thirteen dogs diagnosed with idiopathic IBD, that previously failed to respond TR:TREATMENT_SUMMARY to treatment with elimination diets and metronidazole, were enrolled. All dogs TR:TREATMENT_SUMMARY were treated with prednisone for 8 weeks. Healthy dogs enrolled as controls did TR:TREATMENT_SUMMARY not receive any treatment. #SAMPLEPREP SP:SAMPLEPREP_SUMMARY Fecal samples were lyophilized and approximately 10 mg was sent to the West SP:SAMPLEPREP_SUMMARY Coast Metabolomics Center (WCMC) at University of California at Davis SP:SAMPLEPREP_SUMMARY (http://metabolomics.ucdavis.edu/). Samples were analyzed on a gas SP:SAMPLEPREP_SUMMARY chromatography time-of-flight mass spectrometry (GC–TOF–MS) platform, in SP:SAMPLEPREP_SUMMARY accordance with published methods. Briefly, samples underwent homogenization and SP:SAMPLEPREP_SUMMARY extraction, followed by centrifugation. Dried supernatant was resuspended in SP:SAMPLEPREP_SUMMARY methanol/chloroform and internal standards were added, followed by drying and SP:SAMPLEPREP_SUMMARY derivatization by methoxyamine hydrochloride and SP:SAMPLEPREP_SUMMARY N-methyl-N-trimethylsilyltrifluoroacetamide. A volume of 0.5 μL was injected in SP:SAMPLEPREP_SUMMARY splitless mode onto a Restek rtx5SilMS column on a temperature-gradient SP:SAMPLEPREP_SUMMARY programmed GC (oven 50–330 °C at 20 °C/min, injector 50–250 °C at 12 °C/ SP:SAMPLEPREP_SUMMARY sec) coupled with a Leco Pegasus IV mass spectrometer (scanning 70 spectra/sec SP:SAMPLEPREP_SUMMARY from 80 to 500 Da, −70 eV ionization energy, 1800 V detector voltage) with SP:SAMPLEPREP_SUMMARY helium carrier gas (1 mL/min). Raw data files were processed using ChromaTOF v. SP:SAMPLEPREP_SUMMARY 2.32. BinBase algorithm matched spectra to database compounds, and SP:SAMPLEPREP_SUMMARY quantification was reported by peak height of an ion at the specific retention SP:SAMPLEPREP_SUMMARY index characteristic of the compound across all samples. Peak heights were SP:SAMPLEPREP_SUMMARY normalized by average total peak-sums for identified compounds across each SP:SAMPLEPREP_SUMMARY sample group. #CHROMATOGRAPHY CH:CHROMATOGRAPHY_TYPE GC CH:INSTRUMENT_NAME Agilent 6890N CH:COLUMN_NAME Restek Rtx-5Sil MS (30 x 0.25mm, 0.25um) #ANALYSIS AN:ANALYSIS_TYPE MS #MS MS:INSTRUMENT_NAME Leco Pegasus IV TOF MS:INSTRUMENT_TYPE GC-TOF MS:MS_TYPE EI MS:ION_MODE POSITIVE MS:MS_COMMENTS Raw data files are preprocessed directly after data acquisition and stored as MS:MS_COMMENTS ChromaTOF-specific *.peg files, as generic *.txt result files and additionally MS:MS_COMMENTS as generic ANDI MS *.cdf files. ChromaTOF vs. 2.32 is used for data MS:MS_COMMENTS preprocessing without smoothing, 3 s peak width, baseline subtraction just above MS:MS_COMMENTS the noise level, and automatic mass spectral deconvolution and peak detection at MS:MS_COMMENTS signal/noise levels of 5:1 throughout the chromatogram. Apex masses are reported MS:MS_COMMENTS for use in the BinBase algorithm. Result *.txt files are exported to a data MS:MS_COMMENTS server with absolute spectra intensities and further processed by a filtering MS:MS_COMMENTS algorithm implemented in the metabolomics BinBase database. MS:MS_RESULTS_FILE ST001247_AN002071_Results.txt UNITS:peak area Has m/z:Yes Has RT:Yes RT units:Seconds #END