#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