Summary of Study ST001486
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 | ST001486 |
| Study Title | Metabolomics of Ndufs4 KO brain regions (part - VI) |
| Study Summary | Untargeted GC-TOF-MS analysis of Ndufs4 KO and WT mouse cerebellum (CB) |
| 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: | SU001560 |
| 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 |
|---|---|---|
| SA125286 | CBA 15 (35) | KO |
| SA125287 | CBA 20 (14) | KO |
| SA125288 | CBA 23 (38) | KO |
| SA125289 | CBA 13 (34) | KO |
| SA125290 | CBA 21 (36) | KO |
| SA125291 | CBA 8 (33) | KO |
| SA125292 | CBA 3 (27) | KO |
| SA125293 | CBA 5 (29) | KO |
| SA125294 | CBA 7 (32) | KO |
| SA125295 | CBB 26 (41) | KO |
| SA125296 | CBA 11 (3) | KO |
| SA125297 | CBB 27 (42) | KO |
| SA125298 | CBB 37 (16) | KO |
| SA125299 | CBB 40 (19) | KO |
| SA125300 | CBB 42 (21) | KO |
| SA125301 | CBB 45 (24) | KO |
| SA125302 | CBB 36 (15) | KO |
| SA125303 | CBB 33 (E5) | KO |
| SA125304 | CBB 29 (E1) | KO |
| SA125305 | CBB 30 (E2) | KO |
| SA125306 | CBB 32 (E4) | KO |
| SA125307 | CBB 44 (23) | WT |
| SA125308 | CBB 43 (22) | WT |
| SA125309 | CBA 14 (5) | WT |
| SA125310 | CBA 16 (7) | WT |
| SA125311 | CBA 17 (8) | WT |
| SA125312 | CBA 18 (9) | WT |
| SA125313 | CBA 12 (4) | WT |
| SA125314 | CBA 10 (2) | WT |
| SA125315 | CBA 2 (26) | WT |
| SA125316 | CBA 4 (28) | WT |
| SA125317 | CBA 6 (30) | WT |
| SA125318 | CBA 9 (1) | WT |
| SA125319 | CBA 19 (11) | WT |
| SA125320 | CBA 22 (37) | WT |
| SA125321 | CBB 35 (13) | WT |
| SA125322 | CBB 38 (17) | WT |
| SA125323 | CBB 39 (18) | WT |
| SA125324 | CBB 41 (20) | WT |
| SA125325 | CBB 34 (12) | WT |
| SA125326 | CBB 31 (E3) | WT |
| SA125327 | CBB 24 (39) reg | WT |
| SA125328 | CBB 25 (40) | WT |
| SA125329 | CBB 28 (E6) | WT |
| SA125330 | CBA 1 (25) | WT |
| Showing results 1 to 45 of 45 |
Collection:
| Collection ID: | CO001555 |
| 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: | TR001575 |
| Treatment Summary: | The animals did not receive any treatment |
Sample Preparation:
| Sampleprep ID: | SP001568 |
| 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 | AN002463 |
|---|---|
| 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: | CH001805 |
| Instrument Name: | Agilent 7890A |
| Column Name: | Restek Rtx-5Sil (30m x 0.25mm,0.25um) |
| Chromatography Type: | GC |
MS:
| MS ID: | MS002283 |
| Analysis ID: | AN002463 |
| 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 |
| Analysis Protocol File: | Data_processing_method.pdf |
