Summary of Study ST002516
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 | ST002516 |
| Study Title | Time course 2: Growth of Eggerthella lenta in defined media with some samples receiving 13C2 stable isotope labeled acetate |
| Study Type | Untargeted LC-MS |
| Study Summary | This 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. |
| 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 | 2023-03-22 |
| 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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Collection:
| Collection ID: | CO002609 |
| 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. |
| Sample Type: | Bacterial culture supernatant |
| Collection Frequency: | at time points specified in study design table over 64 hours (full growth phase) |
| Storage Conditions: | -80℃ |
