Summary of Study ST003284
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 PR002036. The data can be accessed directly via it's Project DOI: 10.21228/M8FC0Q This work is supported by NIH grant, U2C- DK119886.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
| Study ID | ST003284 |
| Study Title | Quantification of bile acids in amoxicillin treated mice |
| Study Summary | Conventionally housed mice were orally treated with amoxicillin for 24 hours with and without cholic acid (48h) and small intestinal contents were collected for targeted MS analysis. Samples were flash frozen and stored at -80°C prior to analysis. We found that amoxicillin drastically reduced unconjugated and secondary bile acids in the small intestine, while oral cholic acid supplementation produced only a modest recovery in intestinal cholic acid while also reducing the ratio of conjugated to unconjugated bile acids in the small intestine. |
| Institute | Brown University |
| Department | Molecular Microbiology & Immunology |
| Laboratory | Molecular Microbiology & Immunology, Belenky Lab |
| Last Name | Beekman |
| First Name | Chapman |
| Address | BMC 613, 171 Meeting Street, Providence RI 02912 |
| Chapman_Beekman@brown.edu | |
| Phone | 4018635953 |
| Submit Date | 2024-06-20 |
| Num Groups | 4 |
| Total Subjects | 48 |
| Num Females | 48 |
| Analysis Type Detail | LC-MS |
| Release Date | 2024-08-05 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR002036 |
| Project DOI: | doi: 10.21228/M8FC0Q |
| Project Title: | Quantification of intestinal bile acids in Amoxicillin-treated mice |
| Project Summary: | Mice were orally treated with amoxicillin for 24 hours with and without cholic acid (48h) and intestinal bile acids were quantified. |
| Institute: | Brown University |
| Department: | Molecular Microbiology & Immunology |
| Laboratory: | Molecular Microbiology & Immunology, Belenky Lab |
| Last Name: | Beekman |
| First Name: | Chapman |
| Address: | BMC 613, 171 Meeting Street, Providence RI 02912 |
| Email: | Chapman_Beekman@brown.edu |
| Phone: | 4018635953 |
| Funding Source: | NIH |
Subject:
| Subject ID: | SU003404 |
| Subject Type: | Mammal |
| Subject Species: | Mus musculus |
| Taxonomy ID: | 10090 |
| Genotype Strain: | C57/BL6 |
| Age Or Age Range: | 7 weeks |
| Gender: | Female |
| Animal Animal Supplier: | JAX |
Factors:
Subject type: Mammal; Subject species: Mus musculus (Factor headings shown in green)
| mb_sample_id | local_sample_id | Sample source | Treatment |
|---|---|---|---|
| SA356149 | M2 27 | intestinal contents (Small Intestine) | AMX + CA |
| SA356150 | SI 31 T2 | intestinal contents (Small Intestine) | AMX + CA |
| SA356151 | SI 32 T1 | intestinal contents (Small Intestine) | AMX + CA |
| SA356152 | SI 30 T2 | intestinal contents (Small Intestine) | AMX + CA |
| SA356153 | M2 25 | intestinal contents (Small Intestine) | AMX + CA |
| SA356154 | SI 29 T2 | intestinal contents (Small Intestine) | AMX + CA |
| SA356155 | SI 8 T1 | intestinal contents (Small Intestine) | AMX + CA |
| SA356156 | SI 7 T1 | intestinal contents (Small Intestine) | AMX + CA |
| SA356157 | SI 6 T1 | intestinal contents (Small Intestine) | AMX + CA |
| SA356158 | M2 31 | intestinal contents (Small Intestine) | AMX + CA |
| SA356159 | M2 29 | intestinal contents (Small Intestine) | AMX + CA |
| SA356172 | SI 3 T2 | intestinal contents (Small Intestine) | AMX +CA |
| SA356160 | M2 9 | intestinal contents (Small Intestine) | AMX + std. diet |
| SA356161 | M2 11 | intestinal contents (Small Intestine) | AMX + std. diet |
| SA356162 | SI 24 T1 | intestinal contents (Small Intestine) | AMX + std. diet |
| SA356163 | SI 23 T1 | intestinal contents (Small Intestine) | AMX + std. diet |
| SA356164 | SI 22 T1 | intestinal contents (Small Intestine) | AMX + std. diet |
| SA356165 | SI 21 T2 | intestinal contents (Small Intestine) | AMX + std. diet |
| SA356166 | M1 15 | intestinal contents (Small Intestine) | AMX + std. diet |
| SA356167 | M1 13 | intestinal contents (Small Intestine) | AMX + std. diet |
| SA356168 | SI 16 T2 | intestinal contents (Small Intestine) | AMX + std. diet |
| SA356169 | SI 14 T2 | intestinal contents (Small Intestine) | AMX + std. diet |
| SA356170 | SI 13 T1 | intestinal contents (Small Intestine) | AMX + std. diet |
| SA356171 | SI 15 T1 | intestinal contents (Small Intestine) | AMX + std. diet |
| SA356173 | M1 17 | intestinal contents (Small Intestine) | untreated + CA |
| SA356174 | M1 19 | intestinal contents (Small Intestine) | untreated + CA |
| SA356175 | M1 21 | intestinal contents (Small Intestine) | untreated + CA |
| SA356176 | M1 23 | intestinal contents (Small Intestine) | untreated + CA |
| SA356177 | SI 1 T1 | intestinal contents (Small Intestine) | untreated + CA |
| SA356178 | SI 28 T1 | intestinal contents (Small Intestine) | untreated + CA |
| SA356179 | SI 26 T1 | intestinal contents (Small Intestine) | untreated + CA |
| SA356180 | SI 4 T2 | intestinal contents (Small Intestine) | untreated + CA |
| SA356181 | SI 27 T2 | intestinal contents (Small Intestine) | untreated + CA |
| SA356182 | SI 2 T2 | intestinal contents (Small Intestine) | untreated + CA |
| SA356183 | SI 25 T2 | intestinal contents (Small Intestine) | untreated + CA |
| SA356196 | SI 5 T2 | intestinal contents (Small Intestine) | untreated + CA |
| SA356184 | M1 7 | intestinal contents (Small Intestine) | untreated + std. diet |
| SA356185 | M1 5 | intestinal contents (Small Intestine) | untreated + std. diet |
| SA356186 | SI 20 T1 | intestinal contents (Small Intestine) | untreated + std. diet |
| SA356187 | M2 3 | intestinal contents (Small Intestine) | untreated + std. diet |
| SA356188 | SI 18 T2 | intestinal contents (Small Intestine) | untreated + std. diet |
| SA356189 | SI 17 T2 | intestinal contents (Small Intestine) | untreated + std. diet |
| SA356190 | SI 12 T1 | intestinal contents (Small Intestine) | untreated + std. diet |
| SA356191 | SI 11 T1 | intestinal contents (Small Intestine) | untreated + std. diet |
| SA356192 | SI 10 T1 | intestinal contents (Small Intestine) | untreated + std. diet |
| SA356193 | SI 9 T1 | intestinal contents (Small Intestine) | untreated + std. diet |
| SA356194 | M1 1 | intestinal contents (Small Intestine) | untreated + std. diet |
| SA356195 | SI 19 T1 | intestinal contents (Small Intestine) | untreated + std. diet |
| Showing results 1 to 48 of 48 |
Collection:
| Collection ID: | CO003397 |
| Collection Summary: | mice were sacrificed and lumenal contents from select GI organs were collected and immediately flash frozen dry in liquid nitrogen prior to storage at -80°C |
| Sample Type: | Intestine |
Treatment:
| Treatment ID: | TR003413 |
| Treatment Summary: | AMX treatment was administered in drinking water (166.7 µg/mL) for a 24-hour period. This concentration is based on previous studies38,39 and determined to achieve a dosage of approximately 25mg/kg/day. Untreated mice received pH-matched water and both AMX and vehicle solutions were sterile filtered prior to administration. For cholic acid supplementation experiments standard mouse chow was first blended into a course powder using a blender (Vitamix) and 5mg of cholic acid was added per gram of powdered chow. Cholic acid was mixed evenly by re-blending and provided in the powdered chow for a 48-hour period and 24 hours prior to AMX treatment. Control mice received the powdered diet alone and food containers were replaced with fresh powdered diet at 24 hours. |
Sample Preparation:
| Sampleprep ID: | SP003411 |
| Sampleprep Summary: | Calibration samples, study samples, and quality control samples are spiked with a solution of labeled internal standards and subjected to protein precipitation with an organic solvent (acidified methanol). Following centrifugation, an aliquot of the organic supernatant is evaporated to dryness in a gentle stream of nitrogen. The dried extracts are reconstituted and injected onto an Agilent 1290 Infinity / SCIEX QTRAP 6500 LC-MS/MS system equipped with a C18 reverse phase UHPLC column. |
Combined analysis:
| Analysis ID | AN005380 |
|---|---|
| Analysis type | MS |
| Chromatography type | Reversed phase |
| Chromatography system | Agilent 1290 |
| Column | Agilent Eclipse XDB-C18 (100 x 3.0mm); No Particle size information from Metabolon |
| MS Type | ESI |
| MS instrument type | Triple quadrupole |
| MS instrument name | ABI Sciex 6500 QTrap |
| Ion Mode | NEGATIVE |
| Units | ng/mg of sample |
Chromatography:
| Chromatography ID: | CH004079 |
| Chromatography Summary: | Metabolon (Bile acids targeted panel) |
| Instrument Name: | Agilent 1290 |
| Column Name: | Agilent Eclipse XDB-C18 (100 x 3.0mm); No Particle size information from Metabolon |
| Column Temperature: | 40-50 |
| Flow Gradient: | Linear gradient from 5% B to 80% B over 3.35 minutes |
| Flow Rate: | 0.35 mL/min |
| Solvent A: | 100% water; 0.1% formic acid; 0.05% PFPA, pH ~2.5 |
| Solvent B: | 100% methanol; 0.1% formic acid; 0.05% PFPA, pH ~2.5 |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS005109 |
| Analysis ID: | AN005380 |
| Instrument Name: | ABI Sciex 6500 QTrap |
| Instrument Type: | Triple quadrupole |
| MS Type: | ESI |
| MS Comments: | The peak area of each bile acid parent (pseudo-MRM mode) or product ion is measured against the peak area of the respective internal standard parent (pseudo-MRM mode) or product ion. Quantitation is performed using a weighted linear least squares regression analysis generated from fortified calibration standards prepared concurrently with study samples. LC-MS/MS raw data are collected using SCIEX software Analyst 1.7.3 and processed using SCIEX OS-MQ v.3.1.6. Data reduction is performed using Microsoft Excel for Microsoft 365 MSO. |
| Ion Mode: | NEGATIVE |
