Summary of Study ST002969
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 PR001848. The data can be accessed directly via it's Project DOI: 10.21228/M8V42S 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.
| Study ID | ST002969 |
| Study Title | Polar metabolites in cecal tissue of mice treated with or without ampicillin and tributyrin |
| Study Summary | The chromatin landscape integrates diverse cellular signals to regulate genome structure and subsequent biological functions, partly through posttranslational modifications (PTMs) on histone proteins. Many donor molecules for histone PTMs are metabolites and are therefore impacted by cellular metabolism and environmental cues. In this study, we aimed to investigate how chromatin and cellular metabolism are linked in the intestine. One class of metabolites in intestinal lumen is short chain fatty acids (SCFAs), which are generated by the commensal microbiota. We found that select histone PTMs (including acetylation, butyrylation, and propionylation) are located in intestinal epithelial cells and are dependent on the presence of microbes. Histone butyrylation is associated with active gene expression and regulated by the metabolite tributyrin, which increases metabolites related to butyrate metabolism and induces specific metabolic gene programs. Together, these studies demonstrate a physiological setting in which previously uncharacterized histone acylations are dynamically regulated through metabolites and associated with gene expression. |
| Institute | Case Western Reserve University |
| Department | Biochemistry |
| Laboratory | Gates |
| Last Name | Gates |
| First Name | Leah |
| Address | Wood Building W456, 2109 Adelbert Road, Cleveland, Ohio 44106-4395 |
| leah.gates@case.edu | |
| Phone | 216-368-5572 |
| Submit Date | 2023-08-28 |
| Num Groups | 3 |
| Total Subjects | 15 |
| Num Females | 15 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzXML |
| Analysis Type Detail | LC-MS |
| Release Date | 2023-12-04 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR001848 |
| Project DOI: | doi: 10.21228/M8V42S |
| Project Title: | Polar metabolites in cecal tissue of mice treated with or without ampicillin and tributyrin |
| Project Summary: | Polar metabolites were profiled in cecal tissue isolated from 8 week old female C57BL/6 mice treated with or without 1g/L ampicillin in drinking water and 200 ul tributyrin gavage. |
| Institute: | Case Western Reserve University |
| Department: | Biochemistry |
| Laboratory: | Gates |
| Last Name: | Gates |
| First Name: | Leah |
| Address: | Wood Building W456, 2109 Adelbert Road, Cleveland, Ohio 44106-4395 |
| Email: | leah.gates@case.edu |
| Phone: | 216-368-5572 |
Subject:
| Subject ID: | SU003082 |
| Subject Type: | Mammal |
| Subject Species: | Mus musculus |
| Taxonomy ID: | 10090 |
| Genotype Strain: | C57BL/6J |
| Age Or Age Range: | 8 weeks |
| Gender: | Female |
| Animal Animal Supplier: | The Jackson Laboratory |
| Animal Housing: | SPF |
| Animal Light Cycle: | 12 hours |
| Animal Feed: | ad libitum |
| Animal Water: | ad libitum |
Factors:
Subject type: Mammal; Subject species: Mus musculus (Factor headings shown in green)
| mb_sample_id | local_sample_id | Treatment |
|---|---|---|
| SA323036 | Cecum_AM_m7 | Ampicillin_Mock |
| SA323037 | Cecum_AM_m9 | Ampicillin_Mock |
| SA323038 | Cecum_AM_m10 | Ampicillin_Mock |
| SA323039 | Cecum_AM_m6 | Ampicillin_Mock |
| SA323040 | Cecum_AM_m8 | Ampicillin_Mock |
| SA323041 | Cecum_AT_m13 | Ampicillin_Tributyrin |
| SA323042 | Cecum_AT_m14 | Ampicillin_Tributyrin |
| SA323043 | Cecum_AT_m15 | Ampicillin_Tributyrin |
| SA323044 | Cecum_AT_m12 | Ampicillin_Tributyrin |
| SA323045 | Cecum_AT_m11 | Ampicillin_Tributyrin |
| SA323046 | Cecum_VM_m2 | Vehicle_Mock |
| SA323047 | Cecum_VM_m1 | Vehicle_Mock |
| SA323048 | Cecum_VM_m4 | Vehicle_Mock |
| SA323049 | Cecum_VM_m3 | Vehicle_Mock |
| SA323050 | Cecum_VM_m5 | Vehicle_Mock |
| Showing results 1 to 15 of 15 |
Collection:
| Collection ID: | CO003075 |
| Collection Summary: | Intestine sections were extracted, cleaned of all feces, washed in cold PBS, and then flash-frozen in liquid nitrogen. |
| Sample Type: | Cecum |
Treatment:
| Treatment ID: | TR003091 |
| Treatment Summary: | Treatment groups are: vehicle-treated with mock gavage (Vehicle_Mock or VM), ampicillin-treated with mock gavage (Ampicillin_Mock or AM), or ampicillin-treated with tributyrin gavage (Ampicillin_Tributyrin or AT). In summary, mice were allowed to acclimate to water with 10g/L Splenda in drinking tubes for at least one day. Water was then switched to either Splenda alone (vehicle, n=5) or Splenda plus 1g/L ampicillin (Sigma catalogue# A1593; ampicillin, n=10). Mice were treated for seven days with this drinking water, and water was changed at least every several days. On day 7, mice were fasted for 4 hours and then gavaged with either 200 ul tributyrin (Sigma catalogue# W222305; n=5 of ampicillin treated group) or mock (25% glycerol, n=5 of ampicillin treated group and n=5 of vehicle treated group). Mice were sacrificed 6 hours following gavage for tissue harvesting. |
Sample Preparation:
| Sampleprep ID: | SP003088 |
| Sampleprep Summary: | Samples were grinded in a mortar and pestle in liquid nitrogen and then weighed on an analytical scale. Polar metabolites were extracted in equal weight/volume 80% methanol that included 15N and 13C fully-labeled amino acid standards (MSK-A2-1.2, Cambridge Isotope Laboratories, Inc). Samples were shaken for ten minutes in the cold room and then centrifuged at 16,000xg for ten minutes to remove debris and proteins. Samples were then dried under nitrogen and stored at -80°C until analysis by liquid chromatography mass spectrometry (LC-MS). |
Combined analysis:
| Analysis ID | AN004878 |
|---|---|
| Analysis type | MS |
| Chromatography type | HILIC |
| Chromatography system | Thermo QExactive orbitrap |
| Column | EMD Millipore ZIC-pHILIC (150 x 2.1mm, 5μm) |
| MS Type | ESI |
| MS instrument type | Orbitrap |
| MS instrument name | Thermo Q Exactive Orbitrap |
| Ion Mode | UNSPECIFIED |
| Units | Normalized Area |
Chromatography:
| Chromatography ID: | CH003680 |
| Instrument Name: | Thermo QExactive orbitrap |
| Column Name: | EMD Millipore ZIC-pHILIC (150 x 2.1mm, 5μm) |
| Column Temperature: | 40 |
| Flow Gradient: | 0-22 min linear gradient from 90% to 40% B; 22-24 min: held at 40% B; 24-24.1 min: returned to 90% B; 24.1-30 min: equilibrated at 90% B. |
| Flow Rate: | 0.150 mL/min |
| Solvent A: | 20 mM ammonium carbonate with 0.1% (v/v) ammonium hydroxide (adjusted to pH 9.3) |
| Solvent B: | 100% acetonitrile |
| Chromatography Type: | HILIC |
MS:
| MS ID: | MS004622 |
| Analysis ID: | AN004878 |
| Instrument Name: | Thermo Q Exactive Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | The mass spectrometer was operated with a spray voltage set to 3.5 kV and heated capillary temperature of 350°C. Polarity switching method was used. MS1 data was acquired with the scan ranges of 55-440 and 438-876 m/z. Software used include XCalibur QualBrowser 2.2 and Skyline Targeted Mass Spec Environment. The metabolite data are normalized to median metabolite signal. Specifically, metabolites with >8% background signal was subtracted, a mean internal standard normalization was performed to correct for observed differences in internal standard signals across samples, and the samples were normalized to the median metabolite signal. |
| Ion Mode: | UNSPECIFIED |
