Summary of Study ST002237
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 PR001427. The data can be accessed directly via it's Project DOI: 10.21228/M88D9X 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 | ST002237 |
| Study Title | Metabolomic analysis of brain cortex from neuronal specific Depdc5 knockout in fed and fasting state |
| Study Type | Depdc5 KO fed vs. fasted comparison |
| Study Summary | Caloric restriction and acute fasting are known to reduce seizures but through unclear mechanisms. In this study, we demonstrate that mTORC1 signaling is reduced after acute fasting of mice. In neurons, mTORC1 is most sensitive to withdrawal of leucine, arginine, and glutamine, which is dependent on DEPDC5. We performed metabolomic analysis of brain cortex from neuronal specific Depdc5 knockout in fed and fasting state. The Depdc5 neuronal specific knockout mice are resistant to sensing significant fluctuations in brain amino acid levels after fasting. These results establish that acute fasting reduces seizure susceptibility in a DEPDC5-dependent manner. |
| Institute | Northwestern University, Feinberg School of Medicine |
| Department | Medicine |
| Laboratory | Chandel Lab |
| Last Name | Chandel |
| First Name | Navdeep |
| Address | 303 E Superior St, Chicago, Illinois, 60611, USA |
| nav@northwestern.edu | |
| Phone | 3125032549 |
| Submit Date | 2022-07-27 |
| Num Groups | 4 |
| Total Subjects | 40 |
| Num Males | 20 |
| Num Females | 20 |
| Publications | DEPDC5-dependent mTORC1 signaling mechanisms are critical for the anti-seizure effects of acute fasting |
| Raw Data Available | Yes |
| Raw Data File Type(s) | raw(Thermo) |
| Analysis Type Detail | LC-MS |
| Release Date | 2022-08-15 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Combined analysis:
| Analysis ID | AN003650 |
|---|---|
| Analysis type | MS |
| Chromatography type | HILIC |
| Chromatography system | Thermo Dionex Ultimate 3000 |
| Column | Waters Xbridge Amide (100 x 3mm,3.5um) |
| MS Type | ESI |
| MS instrument type | Orbitrap |
| MS instrument name | Thermo Q Exactive Orbitrap |
| Ion Mode | UNSPECIFIED |
| Units | Peak area |
Chromatography:
| Chromatography ID: | CH002704 |
| Chromatography Summary: | Samples were analyzed by High-Performance Liquid Chromatography and High-Resolution Mass Spectrometry and Tandem Mass Spectrometry (HPLC-MS/MS). Specifically, system consisted of a Thermo Q-Exactive in line with an electrospray source and an Ultimate3000 (Thermo) series HPLC consisting of a binary pump, degasser, and auto-sampler outfitted with a Xbridge Amide column (Waters; dimensions of 3.0 mm × 100 mm and a 3.5 µm particle size). The mobile phase A contained 95% (vol/vol) water, 5% (vol/vol) acetonitrile, 10 mM ammonium hydroxide, 10 mM ammonium acetate, pH = 9.0; B was 100% Acetonitrile. The gradient was as following: 0 min, 15% A; 2.5 min, 30% A; 7 min, 43% A; 16 min, 62% A; 16.1-18 min, 75% A; 18-25 min, 15% A with a flow rate of 150 μL/min. The capillary of the ESI source was set to 275 °C, with sheath gas at 35 arbitrary units, auxiliary gas at 5 arbitrary units and the spray voltage at 4.0 kV. In positive/negative polarity switching mode, an m/z scan range from 60 to 900 was chosen and MS1 data was collected at a resolution of 70,000. The automatic gain control (AGC) target was set at 1 × 106 and the maximum injection time was 200 ms. The top 5 precursor ions were subsequently fragmented, in a data-dependent manner, using the higher energy collisional dissociation (HCD) cell set to 30% normalized collision energy in MS2 at a resolution power of 17,500. Besides matching m/z, metabolites are identified by matching either retention time with analytical standards and/or MS2 fragmentation pattern. Data acquisition and analysis were carried out by Xcalibur 4.1 software and Tracefinder 4.1 software, respectively (both from Thermo Fisher Scientific). |
| Instrument Name: | Thermo Dionex Ultimate 3000 |
| Column Name: | Waters Xbridge Amide (100 x 3mm,3.5um) |
| Flow Gradient: | 0 min, 15% A; 2.5 min, 30% A; 7 min, 43% A; 16 min, 62% A; 16.1-18 min, 75% A; 18-25 min, 15% A |
| Flow Rate: | 150 µL/min |
| Solvent A: | 95% water/5% acetonitrile; 10 mM ammonium hydroxide; 10 mM ammonium acetate, pH 9.0 |
| Solvent B: | 100% acetonitrile |
| Chromatography Type: | HILIC |
