Summary of Study ST002512
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 PR001620. The data can be accessed directly via it's Project DOI: 10.21228/M89B04 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 | ST002512 |
Study Title | Gnotobiotic mice: Metabolites in intestinal contents of germ-free mice colonized with strains of gut bacterium Eggerthella lenta |
Study Type | Untargeted LC-MS |
Study Summary | This dataset contains untargeted metabolomics analysis of intestinal contents of gnotobiotic mice either colonized with different strains of Eggerthella lenta for 2 weeks, or germ-free controls. |
Institute | University of California, San Francisco |
Last Name | Noecker |
First Name | Cecilia |
Address | 513 Parnassus Ave HSW1501, San Francisco, CA 94143 |
cecilia.noecker@ucsf.edu | |
Phone | 415-502-3264 |
Submit Date | 2023-03-21 |
Raw Data Available | Yes |
Raw Data File Type(s) | mzML, raw(Thermo) |
Analysis Type Detail | LC-MS |
Release Date | 2023-04-10 |
Release Version | 1 |
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Sample Preparation:
Sampleprep ID: | SP002618 |
Sampleprep Summary: | Intestinal samples (colon, cecum, ileum) were prepared individually using a single protocol as follows. Samples were kept frozen on dry ice and massed to at least 10 mg. Four microliters of -20oC extraction solvent (2:2:1 methanol:acetonitrile:water + stable isotope labeled internal standards) were added per milligram of intestinal sample. Six to eight 1mm zirconia silica beads were added to each sample followed by prompt bead beating (15 Hz, for 10 minutes). Following a 1 hour incubation in the -20oC freezer, samples were centrifuged at 4oC at 18,407 rcf for 5 minutes. Supernatant was collected and stored at -20oC prior to centrifugal plate filtration (0.2 micron polyvinylidene difluoride (PVDF) Agilent Technologies, Santa Clara CA) at 4oC at 4,122 rcf for 3 min. Collection plate was sealed and maintained at 4oC prior to prompt analysis. Serum samples were first thawed on wet ice. 20 μL of serum was extracted with 4 volumes of methanol, containing stable isotope labeled internal standards. Samples were homogenized by vortexing for 20 seconds and placed in a -20oC for 1 hour to maximize protein precipitation. After freezer incubation, samples were centrifuged at 4oC at 18,407 rcf for 5 minutes. Supernatant was removed and dried under vacuum via centrivap (Labconco Corp.). Dried samples were then resuspended in 30 μL of 80% acetonitrile in water containing exogenous standard CUDA at 60 ng/mL. Samples were maintained at 4oC prior to prompt analysis. |