Summary of Study ST001483
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
| Study ID | ST001483 |
| Study Title | Metabolomics of Ndufs4 KO brain regions (part - III) |
| Study Summary | Targeted LC-MS/MS analysis of amino acids and acylcarnitines in 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) | d |
| Analysis Type Detail | LC-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: | SU001557 |
| 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 |
|---|---|---|
| SA125146 | BST1 15 (15) | KO |
| SA125147 | BST1 16 (16) | KO |
| SA125148 | BST1 21 (21) | KO |
| SA125149 | BST1 12 (14) | KO |
| SA125150 | BST1 19 (19) | KO |
| SA125151 | BST1 5 (24) | KO |
| SA125152 | BST1 1 (E1) | KO |
| SA125153 | BST1 2 (E2) | KO |
| SA125154 | BST1 4 (E4) | KO |
| SA125155 | BST2 27 (27) | KO |
| SA125156 | BST1 9 (10) | KO |
| SA125157 | BST2 29 (29) | KO |
| SA125158 | BST2 40 (41) | KO |
| SA125159 | BST2 45 (3) | KO |
| SA125160 | BST2 41 (42) redo | KO |
| SA125161 | BST2 38 (38) | KO |
| SA125162 | BST2 37 (36) | KO |
| SA125163 | BST2 31 (34) | KO |
| SA125164 | BST2 32 (32) | KO |
| SA125165 | BST2 33 (33) | KO |
| SA125166 | BST2 35 (35) | KO |
| SA125167 | BST2 47 (5) | WT |
| SA125168 | BST2 46 (4) | WT |
| SA125169 | BST2 44 (2) | WT |
| SA125170 | BST1 14 (13) | WT |
| SA125171 | BST1 18 (18) | WT |
| SA125172 | BST1 20 (20) | WT |
| SA125173 | BST1 21 (17) redo | WT |
| SA125174 | BST1 13 (12) | WT |
| SA125175 | BST1 11 (11) | WT |
| SA125176 | BST1 6 (E6) | WT |
| SA125177 | BST1 7 (7) | WT |
| SA125178 | BST1 8 (8) | WT |
| SA125179 | BST1 10 (9) | WT |
| SA125180 | BST1 22 (22) | WT |
| SA125181 | BST1 23 (23) | WT |
| SA125182 | BST2 39 (39) | WT |
| SA125183 | BST2 39 (39) after clean | WT |
| SA125184 | BST2 42 (40) | WT |
| SA125185 | BST2 43 (1) | WT |
| SA125186 | BST2 36 (37) | WT |
| SA125187 | BST2 34 (31) | WT |
| SA125188 | BST2 25 (25) | WT |
| SA125189 | BST2 26 (26) | WT |
| SA125190 | BST2 28 (28) | WT |
| SA125191 | BST2 30 (30) | WT |
| SA125192 | BST1 3 (E3) | WT |
| Showing results 1 to 47 of 47 |
Collection:
| Collection ID: | CO001552 |
| 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: | TR001572 |
| Treatment Summary: | The animals did not receive any treatment |
Sample Preparation:
| Sampleprep ID: | SP001565 |
| Sampleprep Summary: | Brain regions were homogenized in the presence of internal standards using a vibration mill. Metabolite extraction was achieved using a biphasic Bligh–Dyer extraction method (methanol/water/chloroform, 2:1.8:2). The polar phases of biphasic extracts were used for LC-MS/MS analysis |
| Sampleprep Protocol Filename: | GC_sample_prep_protocol.pdf Data_processing_method.pdf |
Combined analysis:
| Analysis ID | AN002460 |
|---|---|
| Analysis type | MS |
| Chromatography type | Reversed phase |
| Chromatography system | Agilent 1200 |
| Column | Agilent C18 Zorbax SB-AQ (150 x 2.1mm,3.5 um) |
| MS Type | ESI |
| MS instrument type | Triple quadrupole |
| MS instrument name | Agilent 6410A QQQ |
| Ion Mode | POSITIVE |
| Units | Area |
Chromatography:
| Chromatography ID: | CH001802 |
| Instrument Name: | Agilent 1200 |
| Column Name: | Agilent C18 Zorbax SB-AQ (150 x 2.1mm,3.5 um) |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS002280 |
| Analysis ID: | AN002460 |
| Instrument Name: | Agilent 6410A QQQ |
| Instrument Type: | Triple quadrupole |
| MS Type: | ESI |
| MS Comments: | The Agilent© MassHunter Workstation (v B02.01) and MassHunter Optimiser (v B02.01) software were used for data acquisition in the multiple reaction monitoring (MRM) configuration setting with parameters set for target amino acids, -derivatives, acylcarnitines, and isotopes. Data extraction was done using the Agilent© MassHunter Workstation software (v B06.00; Qualitative Analysis and Quantitative Analysis) |
| Ion Mode: | POSITIVE |
