Summary of Study ST001484
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 PR001003. The data can be accessed directly via it's Project DOI: 10.21228/M8210V 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 | ST001484 |
| Study Title | Metabolomics of Ndufs4 KO brain regions (part - IV) |
| Study Summary | Untargeted GC-TOF-MS analysis of Ndufs4 KO and WT mouse brain stem (BST) |
| Institute | North-West University |
| Last Name | Louw |
| First Name | Roan |
| Address | Hofman Street |
| Roan.Louw@nwu.ac.za | |
| Phone | +27 18 299 4074 |
| Submit Date | 2020-09-11 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | peg |
| Analysis Type Detail | GC-MS |
| Release Date | 2021-09-10 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR001003 |
| Project DOI: | doi: 10.21228/M8210V |
| Project Title: | Ndufs4 KO mouse model metabolomics studies |
| Project Type: | Multi-platform metabolomics analysis |
| Project Summary: | Multi-platform metabolomics analysis of tissues and biofluids from the Ndufs4 knockout (Ndufs4-/-) mouse model of human Leigh syndrome |
| Institute: | North-West University |
| Last Name: | Louw |
| First Name: | Roan |
| Address: | Hofman Street |
| Email: | Roan.Louw@nwu.ac.za |
| Phone: | +27 18 299 4074 |
Subject:
| Subject ID: | SU001558 |
| Subject Type: | Mammal |
| Subject Species: | Mus musculus |
| Taxonomy ID: | 10090 |
| Genotype Strain: | Ndufs4, https://www.jax.org/strai n/02705 8 |
| Age Or Age Range: | 45-50 days |
| Gender: | Male |
| Animal Animal Supplier: | Jackson Laboratory (ME, USA) |
| Animal Light Cycle: | 12:12 h |
| Animal Feed: | Rodent Breeder, Cat. #RM1845, LabChef, Nutritionhub |
| Animal Water: | ad libitum |
Factors:
Subject type: Mammal; Subject species: Mus musculus (Factor headings shown in green)
| mb_sample_id | local_sample_id | Genotype |
|---|---|---|
| SA125193 | BST1 21 | KO |
| SA125194 | BST1 24 | KO |
| SA125195 | BST2 29 | KO |
| SA125196 | BST1 19 | KO |
| SA125197 | BST2 27 | KO |
| SA125198 | BST1 15 | KO |
| SA125199 | BST1 3 | KO |
| SA125200 | BST1 10 | KO |
| SA125201 | BST1 14 | KO |
| SA125202 | BST2 32 | KO |
| SA125203 | BST1 16 | KO |
| SA125204 | BST2 33 | KO |
| SA125205 | BST2 42 | KO |
| SA125206 | BST2 E 1 | KO |
| SA125207 | BST2 E 2 | KO |
| SA125208 | BST2 E 4 | KO |
| SA125209 | BST2 41 | KO |
| SA125210 | BST2 38 | KO |
| SA125211 | BST2 34 | KO |
| SA125212 | BST2 35 | KO |
| SA125213 | BST2 36 | KO |
| SA125214 | BST2 E 6 | WT |
| SA125215 | BST2 E 3 | WT |
| SA125216 | BST1 11 | WT |
| SA125217 | BST1 12 | WT |
| SA125218 | BST1 13 | WT |
| SA125219 | BST1 17 | WT |
| SA125220 | BST1 9 | WT |
| SA125221 | BST1 8 | WT |
| SA125222 | BST1 2 | WT |
| SA125223 | BST1 4 | WT |
| SA125224 | BST1 5 | WT |
| SA125225 | BST1 7 | WT |
| SA125226 | BST1 18 | WT |
| SA125227 | BST1 20 | WT |
| SA125228 | BST2 31 | WT |
| SA125229 | BST2 37 | WT |
| SA125230 | BST2 39 | WT |
| SA125231 | BST2 40 | WT |
| SA125232 | BST2 30 | WT |
| SA125233 | BST2 28 | WT |
| SA125234 | BST1 22 | WT |
| SA125235 | BST1 23 | WT |
| SA125236 | BST2 25 | WT |
| SA125237 | BST2 26 | WT |
| SA125238 | BST1 1 | WT |
| Showing results 1 to 46 of 46 |
Collection:
| Collection ID: | CO001553 |
| Collection Summary: | Mice were euthanized between postnatal day (P) 45-50 via cervical dislocation at the same time of day (8:00-9:00 AM) after overnight (12-h) fasting. The brain was removed and rinsed with saline solution (SABAX PBS; 0.9% NaCl (w/v), #7634, Adcock Ingram) to remove surrounding blood. The brain regions of interest, namely the anterior cortex (AC), brainstem (BS), cerebellum (CB) and olfactory bulbs (OB), were then dissected, snap-frozen in liquid nitrogen (within 15 minutes postmortem) and stored at − 80°C until used. |
| Sample Type: | Brain |
Treatment:
| Treatment ID: | TR001573 |
| Treatment Summary: | The animals did not receive any treatment |
Sample Preparation:
| Sampleprep ID: | SP001566 |
| Sampleprep Summary: | Brain regions were homogenized in the presence of internal standards using a vibration mill. Metabolite extraction was achieved using a modified monophasic Bligh–Dyer extraction method with a solvent ratio of 3:1:1 (methanol:water:chloroform). |
| Sampleprep Protocol Filename: | GC_sample_prep_protocol.pdf Data_processing_method.pdf |
Combined analysis:
| Analysis ID | AN002461 |
|---|---|
| Analysis type | MS |
| Chromatography type | GC |
| Chromatography system | Agilent 7890A |
| Column | Restek Rtx-5Sil (30m x 0.25mm,0.25um) |
| MS Type | EI |
| MS instrument type | GC-TOF |
| MS instrument name | Leco Pegasus HT TOF |
| Ion Mode | POSITIVE |
| Units | Area |
Chromatography:
| Chromatography ID: | CH001803 |
| Instrument Name: | Agilent 7890A |
| Column Name: | Restek Rtx-5Sil (30m x 0.25mm,0.25um) |
| Chromatography Type: | GC |
MS:
| MS ID: | MS002281 |
| Analysis ID: | AN002461 |
| Instrument Name: | Leco Pegasus HT TOF |
| Instrument Type: | GC-TOF |
| MS Type: | EI |
| MS Comments: | The LECO Corporation ChromaTOF® software (v 4.5x) was used for data acquisition and extraction. This included automatic baseline removal via the “spanning” tracking method (offset of 1; just above the noise) and auto smoothing, with the software’s Statistical Compare feature used to align peaks. Spectral matching was done using the NIST11 commercial library and an in-house mass spectral library in order to identify important analytes. |
| Ion Mode: | POSITIVE |
