Summary of Study ST001488
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 | ST001488 |
| Study Title | Metabolomics of Ndufs4 KO brain regions (part - VIII) |
| Study Summary | Untargeted GC-TOF-MS analysis of Ndufs4 KO and WT mouse olfactory bulbs (OB) |
| 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: | SU001562 |
| 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 |
|---|---|---|
| SA125373 | OB1 19 | KO |
| SA125374 | OB1 21 | KO |
| SA125375 | OB2 27 | KO |
| SA125376 | OB1 16 | KO |
| SA125377 | OB1 24 | KO |
| SA125378 | OB1 15 | KO |
| SA125379 | OB1 3 | KO |
| SA125380 | OB1 10 | KO |
| SA125381 | OB1 14 | KO |
| SA125382 | OB2 29 | KO |
| SA125383 | OB2 32 | KO |
| SA125384 | OB2 41 | KO |
| SA125385 | OB2 42 | KO |
| SA125386 | OB2 E 4 | KO |
| SA125387 | OB2 38 | KO |
| SA125388 | OB2 36 | KO |
| SA125389 | OB2 33 | KO |
| SA125390 | OB2 34 | KO |
| SA125391 | OB2 35 | KO |
| SA125392 | OB2 40 | WT |
| SA125393 | OB2 39 | WT |
| SA125394 | OB1 9 | WT |
| SA125395 | OB1 11 | WT |
| SA125396 | OB1 12 | WT |
| SA125397 | OB1 13 | WT |
| SA125398 | OB1 8 | WT |
| SA125399 | OB1 7 | WT |
| SA125400 | OB1 2 | WT |
| SA125401 | OB1 4 | WT |
| SA125402 | OB1 5 | WT |
| SA125403 | OB1 17 | WT |
| SA125404 | OB1 18 | WT |
| SA125405 | OB2 28 | WT |
| SA125406 | OB2 30 | WT |
| SA125407 | OB2 31 | WT |
| SA125408 | OB2 37 | WT |
| SA125409 | OB2 26 | WT |
| SA125410 | OB2 25 | WT |
| SA125411 | OB1 20 | WT |
| SA125412 | OB1 22 | WT |
| SA125413 | OB1 23 | WT |
| SA125414 | OB1 1 | WT |
| Showing results 1 to 42 of 42 |
Collection:
| Collection ID: | CO001557 |
| 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: | TR001577 |
| Treatment Summary: | The animals did not receive any treatment |
Sample Preparation:
| Sampleprep ID: | SP001570 |
| Sampleprep Summary: | BBrain 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 | AN002465 |
|---|---|
| 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 GC-TOF |
| Ion Mode | POSITIVE |
| Units | area |
Chromatography:
| Chromatography ID: | CH001807 |
| Instrument Name: | Agilent 7890A |
| Column Name: | Restek Rtx-5Sil (30m x 0.25mm,0.25um) |
| Chromatography Type: | GC |
MS:
| MS ID: | MS002285 |
| Analysis ID: | AN002465 |
| Instrument Name: | Leco GC-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 |
