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
Email	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

Select appropriate tab below to view additional metadata details:

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.

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.