Summary of Study ST002517

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench,, 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.


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 IDST002517
Study TitleTime course 2: Growth of Eggerthella lenta in defined media with some samples receiving 13C2 stable isotope labeled acetate (intracellular samples)
Study TypeUntargeted LC-MS
Study SummaryThis dataset contains untargeted metabolomics analysis of supernatants from 3 strains of Eggerthella lenta grown in defined EDM1 media with varying acetate concentrations. One set of samples grew in EDM1 containing 13C2 stable isotope labeled acetate. Samples were collected at a subset of time points for extraction of intracellular metabolites.
University of California, San Francisco
Last NameNoecker
First NameCecilia
Address513 Parnassus Ave HSW1501, San Francisco, CA 94143
Submit Date2023-03-22
Raw Data AvailableYes
Raw Data File Type(s)mzML, raw(Thermo)
Analysis Type DetailLC-MS
Release Date2023-04-10
Release Version1
Cecilia Noecker Cecilia Noecker application/zip

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Collection ID:CO002610
Collection Summary:Time course experiments were conducted in tubes in the anaerobic chamber in a 37°C incubator. For all metabolomics experiments, three independent culture replicates were included for each condition, with an equal number of uninoculated control tubes. Starter cultures and inocula were prepared as described above for growth assays. 5mLs of defined media was added to VWR glass culture tubes (53283-800) with screw caps. The PBS-washed inoculum was added to culture tubes to obtain an approximate starting OD600 of 0.001. A preliminary growth assay was conducted to define time points spanning the exponential growth phase in the tested conditions. At each time point, OD600 measurements of all inoculated tubes were first measured using a Hach DR1900 spectrophotometer, with a paired control tube to normalize for the background. 100 μL from each tube were then transferred into a 96-well microplate, which was sealed and removed from the anaerobic chamber. Plates were centrifuged at 1,928 rcf at 4°C for 8 minutes, after which supernatants were collected into fresh polypropylene tubes or plates, sealed, and flash-frozen in liquid nitrogen. Two time course experiments were carried out with stable isotope-labeled substrates. Experimental groups included conditions in which sodium acetate in the defined media was replaced with 13C2 labeled sodium acetate (Sigma-Aldrich 282014), along with a matched experimental group with the same concentration of unlabeled substrate. Intracellular extract samples were prepared with the following procedure, which was optimized for lysis of thick gram-positive cell walls: 600 μL of culture was transferred to an Eppendorf tube in anaerobic conditions and subsequently centrifuged at 10,000rcf for three minutes at 4°C, after which the supernatant was removed and the samples were immediately flash frozen to quench metabolites. 300 μL of cold methanol was then added to each pellet, followed by sonication on ice for 5 minutes and then shaking at 4°C for 4-12 hours. Samples were then centrifuged at 4°C at 15,000 rcf for 8 minutes, after which 120 μL of supernatant was transferred to fresh tubes and stored at -80°C until analysis.
Sample Type:Bacterial culture supernatant
Collection Frequency:at time points specified in study design table over 64 hours (full growth phase)
Storage Conditions:-80℃