Summary of Study ST001883
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 PR001187. The data can be accessed directly via it's Project DOI: 10.21228/M88M43 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 | ST001883 |
| Study Title | Metabolomics of Ndufs4 KO urine (part - I) |
| Study Summary | Untargeted GC-TOF-MS analysis of Ndufs4 KO and WT mouse urine |
| 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 | 2021-06-30 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | cdf |
| Analysis Type Detail | GC-MS |
| Release Date | 2022-06-30 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR001187 |
| Project DOI: | doi: 10.21228/M88M43 |
| Project Title: | Ndufs4 KO mouse urine metabolomics |
| Project Type: | Multi-platform metabolomics analysis of Ndufs4 KO mouse urine |
| Project Summary: | Multi-platform metabolomics analysis of urine 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: | SU001961 |
| 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 |
|---|---|---|
| SA175090 | 86_3q | KO |
| SA175091 | 96_2i | KO |
| SA175092 | 20_4m | KO |
| SA175093 | 2_3s | KO |
| SA175094 | 42_4q | KO |
| SA175095 | 68_1o | KO |
| SA175096 | 67_2f | KO |
| SA175097 | 18_2l | KO |
| SA175098 | 60_2e | KO |
| SA175099 | 8_4j | KO |
| SA175100 | 44_3k | KO |
| SA175101 | 69_2f | KO |
| SA175102 | 28_3g | KO |
| SA175103 | 34_4o | KO |
| SA175104 | 50_4s | KO |
| SA175105 | 2_4i | KO |
| SA175106 | 56_2d | KO |
| SA175107 | 89_1r | KO |
| SA175108 | 37_3j | KO |
| SA175109 | 10_1v | KO |
| SA175110 | 33_2o | KO |
| SA175111 | 45_3k | KO |
| SA175112 | 54_4a | KO |
| SA175113 | 62_2t | WT |
| SA175114 | 2_1u | WT |
| SA175115 | 65_3n | WT |
| SA175116 | 11_3d | WT |
| SA175117 | 16_4m | WT |
| SA175118 | 91_2i | WT |
| SA175119 | 62_4b | WT |
| SA175120 | 83_3p | WT |
| SA175121 | 8_1v | WT |
| SA175122 | 27_4n | WT |
| SA175123 | 37_4p | WT |
| SA175124 | 82_2g | WT |
| SA175125 | 9_3d | WT |
| SA175126 | 88_3q | WT |
| SA175127 | 9_4j | WT |
| SA175128 | 49_2a | WT |
| SA175129 | 42_3k | WT |
| SA175130 | 68_3n | WT |
| SA175131 | 65_2u | WT |
| SA175132 | 81_3p | WT |
| SA175133 | 53_2c | WT |
| SA175134 | 29_4n | WT |
| SA175135 | 61_2e | WT |
| SA175136 | 63_4b | WT |
| SA175137 | 87_3q | WT |
| SA175138 | 97_4h | WT |
| SA175139 | 98_4h | WT |
| SA175140 | 54_2c | WT |
| SA175141 | 26_3g | WT |
| SA175142 | 57_3l | WT |
| Showing results 1 to 53 of 53 |
Collection:
| Collection ID: | CO001954 |
| Collection Summary: | Urine was collected from individual mice in metabolic cages after overnight (12 hours) fasting with ad libitum access to water. Since Ndufs4 KO mice yielded limited urine volumes, urine droplets that failed to reach the collection tube were also collected. Hence, the separating cone, collection funnel and urine collection tubes were all treated with sodium azide (NaN3; 0.1% w/v; WT: 100 μL and KO: 50 μL) to prevent bacterial growth. Samples were snap-frozen in liquid nitrogen upon collection and stored at −80 °C until used. |
| Sample Type: | Urine |
| Storage Conditions: | -80℃ |
Treatment:
| Treatment ID: | TR001973 |
| Treatment Summary: | The animals did not receive any treatment |
Sample Preparation:
| Sampleprep ID: | SP001967 |
| Sampleprep Summary: | Pre-determined volumes of urine, containing 0.0625 μmole creatinine, were supplemented with internal standards and deproteinized using methanol. Urine samples were then dried under nitrogen and derivatized (methoxymated and silylated) prior to analysis. |
| Sampleprep Protocol Filename: | GC_sample_prep_protocol.pdf |
Combined analysis:
| Analysis ID | AN003047 |
|---|---|
| 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 | mg/g creatinine |
Chromatography:
| Chromatography ID: | CH002257 |
| Methods Filename: | GC_data_acquisition_method.pdf |
| Instrument Name: | Agilent 7890A |
| Column Name: | Restek Rtx-5Sil (30m x 0.25mm,0.25um) |
| Chromatography Type: | GC |
MS:
| MS ID: | MS002834 |
| Analysis ID: | AN003047 |
| 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 |
