Summary of Study ST001247

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR000834. The data can be accessed directly via it's Project DOI: 10.21228/M8W67P This work is supported by NIH grant, U2C- DK119886.

See: https://www.metabolomicsworkbench.org/about/howtocite.php

This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.

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Study IDST001247
Study TitleLongitudinal Characterization of the Fecal Metabolome in Dogs with Idiopathic Inflammatory Bowel Disease
Study SummaryThirteen dogs diagnosed with idiopathic IBD, that previously failed to respond to treatment with elimination diets and metronidazole, were enrolled. 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.
Institute
Texas A&M University
DepartmentDepartment of Small Animal Clinical Sciences
LaboratoryGastrointestinal Laboratory
Last NamePilla
First NameRachel
Address4474 TAMU
Emailrpilla@cvm.tamu.edu
Phone9798622861
Submit Date2019-09-03
Raw Data AvailableYes
Raw Data File Type(s)cdf
Analysis Type DetailMALDI-MS
Release Date2020-06-03
Release Version1
Rachel Pilla Rachel Pilla
https://dx.doi.org/10.21228/M8W67P
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR000834
Project DOI:doi: 10.21228/M8W67P
Project Title:Longitudinal Characterization of the Fecal Metabolome in Dogs with Idiopathic Inflammatory Bowel Disease
Project Summary:Thirteen dogs diagnosed with idiopathic IBD, that previously failed to respond to treatment with elimination diets and metronidazole, were enrolled. 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.
Institute:Texas A&M University
Department:Department of Small Animal Clinical Sciences
Laboratory:Gastrointestinal Laboratory
Last Name:Pilla
First Name:Rachel
Address:4474 TAMU
Email:rpilla@cvm.tamu.edu
Phone:9798622861

Subject:

Subject ID:SU001315
Subject Type:Mammal
Subject Species:Canis lupus familiaris
Taxonomy ID:9615

Factors:

Subject type: Mammal; Subject species: Canis lupus familiaris (Factor headings shown in green)

mb_sample_id local_sample_id Time point
SA090839Healthy_19_0720WK | Status:HC | Treatment:none
SA090840Healthy_18_0710WK | Status:HC | Treatment:none
SA090841Healthy_20_0730WK | Status:HC | Treatment:none
SA090842Healthy_22_0740WK | Status:HC | Treatment:none
SA090843Healthy_23_0750WK | Status:HC | Treatment:none
SA090844Healthy_12_0700WK | Status:HC | Treatment:none
SA090845Healthy_01_0640WK | Status:HC | Treatment:none
SA090846Healthy_06_0680WK | Status:HC | Treatment:none
SA090847Healthy_05_0670WK | Status:HC | Treatment:none
SA090848Healthy_04_0660WK | Status:HC | Treatment:none
SA090849Healthy_02_0650WK | Status:HC | Treatment:none
SA090850Healthy_25_0760WK | Status:HC | Treatment:none
SA090851Healthy_07_0690WK | Status:HC | Treatment:none
SA090852BL_placebo_23_0070WK | Status:IBD | Treatment:none
SA090853BL_placebo_28_0080WK | Status:IBD | Treatment:none
SA090854BL_placebo_20_0060WK | Status:IBD | Treatment:none
SA090855BL_placebo_19_0050WK | Status:IBD | Treatment:none
SA090856BL_placebo_11_0030WK | Status:IBD | Treatment:none
SA090857BL_placebo_14_0040WK | Status:IBD | Treatment:none
SA090858BL_placebo_04_0010WK | Status:IBD | Treatment:none
SA090859BL_placebo_35_0090WK | Status:IBD | Treatment:none
SA090860BL_placebo_07_0020WK | Status:IBD | Treatment:none
SA090861LT_placebo_14_0531YR | Status:IBD | Treatment:none
SA090862LT_placebo_23_0551YR | Status:IBD | Treatment:none
SA090863LT_placebo_28_0561YR | Status:IBD | Treatment:none
SA090864LT_placebo_11_0521YR | Status:IBD | Treatment:none
SA090865LT_placebo_19_0541YR | Status:IBD | Treatment:none
SA0908663WK_placebo_35_0263WK | Status:IBD | Treatment:prednisone
SA0908673WK_placebo_28_0253WK | Status:IBD | Treatment:prednisone
SA0908683WK_placebo_23_0243WK | Status:IBD | Treatment:prednisone
SA0908693WK_placebo_07_0193WK | Status:IBD | Treatment:prednisone
SA0908703WK_placebo_19_0223WK | Status:IBD | Treatment:prednisone
SA0908713WK_placebo_11_0203WK | Status:IBD | Treatment:prednisone
SA0908723WK_placebo_20_0233WK | Status:IBD | Treatment:prednisone
SA0908733WK_placebo_04_0183WK | Status:IBD | Treatment:prednisone
SA0908743WK_placebo_14_0213WK | Status:IBD | Treatment:prednisone
SA0908758WK_placebo_19_0398WK | Status:IBD | Treatment:prednisone
SA0908768WK_placebo_11_0378WK | Status:IBD | Treatment:prednisone
SA0908778WK_placebo_07_0368WK | Status:IBD | Treatment:prednisone
SA0908788WK_placebo_04_0358WK | Status:IBD | Treatment:prednisone
SA0908798WK_placebo_14_0388WK | Status:IBD | Treatment:prednisone
SA0908808WK_placebo_20_0408WK | Status:IBD | Treatment:prednisone
SA0908818WK_placebo_28_0428WK | Status:IBD | Treatment:prednisone
SA0908828WK_placebo_23_0418WK | Status:IBD | Treatment:prednisone
SA0908838WK_placebo_35_0438WK | Status:IBD | Treatment:prednisone
Showing results 1 to 45 of 45

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
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