Summary of Study ST001401
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 PR000961. The data can be accessed directly via it's Project DOI: 10.21228/M8GD71 This work is supported by NIH grant, U2C- DK119886.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
| Study ID | ST001401 |
| Study Title | Steady-state metabolomics time course of Saccharomyces cerevisiae mitochondrial fatty acid synthesis (mtFAS) mutants |
| Study Type | Steady-state targeted and untargeted metabolomics time course |
| Study Summary | The goal of this work was to analyze metabolic changes in yeast at various time points with either the oar1 KO or the mct1 knock-out conditions when compared to a time-matched wild-type samples using gas chromatography-mass spectrometry (GC-MS). |
| Institute | University of Utah |
| Department | Biochemistry |
| Laboratory | Rutter |
| Last Name | Berg |
| First Name | Jordan |
| Address | 15 N Medical Drive East RM 5520, Salt Lake City, UT 84112-5650 USA |
| jordan.berg@biochem.utah.edu | |
| Phone | (801) 581 3340 |
| Submit Date | 2020-06-10 |
| Num Groups | 3 |
| Total Subjects | 95 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | d |
| Analysis Type Detail | GC-MS |
| Release Date | 2020-06-22 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR000961 |
| Project DOI: | doi: 10.21228/M8GD71 |
| Project Title: | Steady-state metabolomics time course of Saccharomyces cerevisiae mitochondrial fatty acid synthesis (mtFAS) mutants |
| Project Type: | Steady-state targeted and untargeted metabolomics time course |
| Project Summary: | The goal of this work was to analyze metabolic changes in yeast at various time points with either the oar1 KO or the mct1 knock-out conditions when compared to a time-matched wild-type samples using gas chromatography-mass spectrometry (GC-MS). MD5 zip archive = a1be9bbea0088a4d21211763d37c49df |
| Institute: | University of Utah |
| Department: | Biochemistry |
| Laboratory: | Rutter Lab |
| Last Name: | Berg |
| First Name: | Jordan |
| Address: | 15 N Medical Drive East RM 5520, Salt Lake City, UT 84112-5650 USA |
| Email: | jordan.berg@biochem.utah.edu |
| Phone: | 678-491-9884 |
| Funding Source: | NIGMS |
| Contributors: | Yeyun Ouyang, Tyler Van Ry, Jordan A. Berg, James E. Cox, Jared Rutter |
Subject:
| Subject ID: | SU001475 |
| Subject Type: | Yeast |
| Subject Species: | Saccharomyces cerevisiae |
| Taxonomy ID: | 4932 |
| Genotype Strain: | BY4743 |
| Gender: | Not applicable |
Factors:
Subject type: Yeast; Subject species: Saccharomyces cerevisiae (Factor headings shown in green)
| mb_sample_id | local_sample_id | Genotype | Treatment | Time |
|---|---|---|---|---|
| SA113818 | mct1KO at 0hr minR+Leu Sample5 | mct1_KO | minR+Leu | 0 min |
| SA113819 | mct1KO at 0hr minR+Leu Sample3 | mct1_KO | minR+Leu | 0 min |
| SA113820 | mct1KO at 0hr minR+Leu Sample4 | mct1_KO | minR+Leu | 0 min |
| SA113821 | mct1KO at 0hr minR+Leu Sample1 | mct1_KO | minR+Leu | 0 min |
| SA113822 | mct1KO at 0hr minR+Leu Sample2 | mct1_KO | minR+Leu | 0 min |
| SA113823 | mct1KO at 0hr minR+Leu Sample6 | mct1_KO | minR+Leu | 0 min |
| SA113824 | mct1KO at 15min minR+Leu Sample2 | mct1_KO | minR+Leu | 15min |
| SA113825 | mct1KO at 15min minR+Leu Sample5 | mct1_KO | minR+Leu | 15min |
| SA113826 | mct1KO at 15min minR+Leu Sample6 | mct1_KO | minR+Leu | 15min |
| SA113827 | mct1KO at 15min minR+Leu Sample4 | mct1_KO | minR+Leu | 15min |
| SA113828 | mct1KO at 15min minR+Leu Sample3 | mct1_KO | minR+Leu | 15min |
| SA113829 | mct1KO at 15min minR+Leu Sample1 | mct1_KO | minR+Leu | 15min |
| SA113830 | mct1KO at 3hr minR+Leu Sample1 | mct1_KO | minR+Leu | 180 min |
| SA113831 | mct1KO at 3hr minR+Leu Sample2 | mct1_KO | minR+Leu | 180 min |
| SA113832 | mct1KO at 3hr minR+Leu Sample3 | mct1_KO | minR+Leu | 180 min |
| SA113833 | mct1KO at 3hr minR+Leu Sample5 | mct1_KO | minR+Leu | 180 min |
| SA113834 | mct1KO at 3hr minR+Leu Sample4 | mct1_KO | minR+Leu | 180 min |
| SA113835 | mct1KO at 3hr minR+Leu Sample6 | mct1_KO | minR+Leu | 180 min |
| SA113836 | mct1KO at 30min minR+Leu Sample5 | mct1_KO | minR+Leu | 30 min |
| SA113837 | mct1KO at 30min minR+Leu Sample2 | mct1_KO | minR+Leu | 30 min |
| SA113838 | mct1KO at 30min minR+Leu Sample4 | mct1_KO | minR+Leu | 30 min |
| SA113839 | mct1KO at 30min minR+Leu Sample6 | mct1_KO | minR+Leu | 30 min |
| SA113840 | mct1KO at 30min minR+Leu Sample3 | mct1_KO | minR+Leu | 30 min |
| SA113841 | mct1KO at 30min minR+Leu Sample1 | mct1_KO | minR+Leu | 30 min |
| SA113842 | mct1KO at 1hr minR+Leu Sample6 | mct1_KO | minR+Leu | 60 min |
| SA113843 | mct1KO at 1hr minR+Leu Sample5 | mct1_KO | minR+Leu | 60 min |
| SA113844 | mct1KO at 1hr minR+Leu Sample3 | mct1_KO | minR+Leu | 60 min |
| SA113845 | mct1KO at 1hr minR+Leu Sample4 | mct1_KO | minR+Leu | 60 min |
| SA113846 | mct1KO at 1hr minR+Leu Sample1 | mct1_KO | minR+Leu | 60 min |
| SA113847 | mct1KO at 1hr minR+Leu Sample2 | mct1_KO | minR+Leu | 60 min |
| SA113848 | oar1 KO at 0hr minR+Leu Sample5 | oar1_KO | minR+Leu | 0 min |
| SA113849 | oar1 KO at 0hr minR+Leu Sample6 | oar1_KO | minR+Leu | 0 min |
| SA113850 | oar1 KO at 0hr minR+Leu Sample4 | oar1_KO | minR+Leu | 0 min |
| SA113851 | oar1 KO at 0hr minR+Leu Sample3 | oar1_KO | minR+Leu | 0 min |
| SA113852 | oar1 KO at 0hr minR+Leu Sample2 | oar1_KO | minR+Leu | 0 min |
| SA113853 | oar1 KO at 0hr minR+Leu Sample1 | oar1_KO | minR+Leu | 0 min |
| SA113854 | oar1 KO at 15min minR+Leu Sample1 | oar1_KO | minR+Leu | 15min |
| SA113855 | oar1 KO at 15min minR+Leu Sample4 | oar1_KO | minR+Leu | 15min |
| SA113856 | oar1 KO at 15min minR+Leu Sample2 | oar1_KO | minR+Leu | 15min |
| SA113857 | oar1 KO at 15min minR+Leu Sample5 | oar1_KO | minR+Leu | 15min |
| SA113858 | oar1 KO at 15min minR+Leu Sample3 | oar1_KO | minR+Leu | 15min |
| SA113859 | oar1 KO at 15min minR+Leu Sample6 | oar1_KO | minR+Leu | 15min |
| SA113860 | oar1 KO at 3hr minR+Leu Sample5 | oar1_KO | minR+Leu | 180 min |
| SA113861 | oar1 KO at 3hr minR+Leu Sample6 | oar1_KO | minR+Leu | 180 min |
| SA113862 | oar1 KO at 3hr minR+Leu Sample4 | oar1_KO | minR+Leu | 180 min |
| SA113863 | oar1 KO at 3hr minR+Leu Sample3 | oar1_KO | minR+Leu | 180 min |
| SA113864 | oar1 KO at 3hr minR+Leu Sample1 | oar1_KO | minR+Leu | 180 min |
| SA113865 | oar1 KO at 3hr minR+Leu Sample2 | oar1_KO | minR+Leu | 180 min |
| SA113866 | oar1 KO at 30min minR+Leu Sample6 | oar1_KO | minR+Leu | 30 min |
| SA113867 | oar1 KO at 30min minR+Leu Sample2 | oar1_KO | minR+Leu | 30 min |
| SA113868 | oar1 KO at 30min minR+Leu Sample3 | oar1_KO | minR+Leu | 30 min |
| SA113869 | oar1 KO at 30min minR+Leu Sample1 | oar1_KO | minR+Leu | 30 min |
| SA113870 | oar1 KO at 30min minR+Leu Sample4 | oar1_KO | minR+Leu | 30 min |
| SA113871 | oar1 KO at 30min minR+Leu Sample5 | oar1_KO | minR+Leu | 30 min |
| SA113872 | oar1 KO at 1hr minR+Leu Sample2 | oar1_KO | minR+Leu | 60 min |
| SA113873 | oar1 KO at 1hr minR+Leu Sample3 | oar1_KO | minR+Leu | 60 min |
| SA113874 | oar1 KO at 1hr minR+Leu Sample6 | oar1_KO | minR+Leu | 60 min |
| SA113875 | oar1 KO at 1hr minR+Leu Sample1 | oar1_KO | minR+Leu | 60 min |
| SA113876 | oar1 KO at 1hr minR+Leu Sample4 | oar1_KO | minR+Leu | 60 min |
| SA113877 | oar1 KO at 1hr minR+Leu Sample5 | oar1_KO | minR+Leu | 60 min |
| SA113878 | PB Sample1 | pb | - | - |
| SA113879 | PB Sample2 | pb | - | - |
| SA113880 | PB Sample3 | pb | - | - |
| SA113881 | QC Sample3 | qc | - | - |
| SA113882 | QC Sample2 | qc | - | - |
| SA113883 | QC Sample1 | qc | - | - |
| SA113884 | WT at 0hr minR+Leu Sample6 | wild-type | minR+Leu | 0 min |
| SA113885 | WT at 0hr minR+Leu Sample1 | wild-type | minR+Leu | 0 min |
| SA113886 | WT at 0hr minR+Leu Sample5 | wild-type | minR+Leu | 0 min |
| SA113887 | WT at 0hr minR+Leu Sample3 | wild-type | minR+Leu | 0 min |
| SA113888 | WT at 0hr minR+Leu Sample4 | wild-type | minR+Leu | 0 min |
| SA113889 | WT at 0hr minR+Leu Sample2 | wild-type | minR+Leu | 0 min |
| SA113890 | WT at 15min minR+Leu Sample4 | wild-type | minR+Leu | 15min |
| SA113891 | WT at 15min minR+Leu Sample5 | wild-type | minR+Leu | 15min |
| SA113892 | WT at 15min minR+Leu Sample3 | wild-type | minR+Leu | 15min |
| SA113893 | WT at 15min minR+Leu Sample1 | wild-type | minR+Leu | 15min |
| SA113894 | WT at 15min minR+Leu Sample6 | wild-type | minR+Leu | 15min |
| SA113895 | WT at 15min minR+Leu Sample2 | wild-type | minR+Leu | 15min |
| SA113896 | WT at 3hr minR+Leu Sample1 | wild-type | minR+Leu | 180 min |
| SA113897 | WT at 3hr minR+Leu Sample2 | wild-type | minR+Leu | 180 min |
| SA113898 | WT at 3hr minR+Leu Sample3 | wild-type | minR+Leu | 180 min |
| SA113899 | WT at 3hr minR+Leu Sample4 | wild-type | minR+Leu | 180 min |
| SA113900 | WT at 3hr minR+Leu Sample5 | wild-type | minR+Leu | 180 min |
| SA113901 | WT at 30min minR+Leu Sample5 | wild-type | minR+Leu | 30 min |
| SA113902 | WT at 30min minR+Leu Sample6 | wild-type | minR+Leu | 30 min |
| SA113903 | WT at 30min minR+Leu Sample1 | wild-type | minR+Leu | 30 min |
| SA113904 | WT at 30min minR+Leu Sample4 | wild-type | minR+Leu | 30 min |
| SA113905 | WT at 30min minR+Leu Sample3 | wild-type | minR+Leu | 30 min |
| SA113906 | WT at 30min minR+Leu Sample2 | wild-type | minR+Leu | 30 min |
| SA113907 | WT at 1hr minR+Leu Sample2 | wild-type | minR+Leu | 60 min |
| SA113908 | WT at 1hr minR+Leu Sample1 | wild-type | minR+Leu | 60 min |
| SA113909 | WT at 1hr minR+Leu Sample3 | wild-type | minR+Leu | 60 min |
| SA113910 | WT at 1hr minR+Leu Sample5 | wild-type | minR+Leu | 60 min |
| SA113911 | WT at 1hr minR+Leu Sample6 | wild-type | minR+Leu | 60 min |
| SA113912 | WT at 1hr minR+Leu Sample4 | wild-type | minR+Leu | 60 min |
| Showing results 1 to 95 of 95 |
Collection:
| Collection ID: | CO001470 |
| Collection Summary: | Metabolomics data were generated by growing the appropriate yeast strains in synthetic minimal media (S-min) supplemented with 2% glucose until they reached OD>600 between 0.6-0.8. Cells were then transferred to S-min media containing 2% raffinose and harvested after 0, 15, 30, 60, and 180 minutes (n=6/time-point/strain; except in one 3 hr wild-type sample, where n=5). |
| Sample Type: | Yeast cells |
| Collection Location: | Rutter Lab, University of Utah |
Treatment:
| Treatment ID: | TR001490 |
| Treatment Summary: | Metabolomics data were generated by growing the appropriate yeast strains in synthetic minimal media (S-min) supplemented with 2% glucose until they reached OD>600 between 0.6-0.8. Cells were then transferred to S-min media containing 2% raffinose and harvested after 0, 15, 30, 60, and 180 minutes (n=6/time-point/strain; except in one 3 hr wild-type sample, where n=5). |
Sample Preparation:
| Sampleprep ID: | SP001483 |
| Sampleprep Summary: | To each sample was added boiling 75% ethanol (EtOH) solution containing the internal standard d4-succinic acid (Sigma 293075). Boiling samples were vortexed and incubated at 90°C for 5 min. Samples were then incubated at -20 ˚C for 1 hr. After incubation the samples were centrifuged at 5,000 x g for 10 minutes at 4˚C. The supernatant was then transferred from each sample tube into a labeled, fresh 13x100mm glass culture tube. A second standard was then added (d27-myristic acid CDN Isotopes: D-1711). Pooled quality control samples were made by removing a fraction of collected supernatant from each sample and process blanks were made using only extraction solvent and no cell culture. The samples were then dried en vacuo. This process was completed in three separate batches. |
Combined analysis:
| Analysis ID | AN002343 |
|---|---|
| Analysis type | MS |
| Chromatography type | GC |
| Chromatography system | Agilent 5977b |
| Column | Phenomenex Zebron AB-5HT (5m) |
| MS Type | EI |
| MS instrument type | Single quadrupole |
| MS instrument name | Agilent 5977 |
| Ion Mode | POSITIVE |
| Units | AUC (unitless) |
Chromatography:
| Chromatography ID: | CH001716 |
| Chromatography Summary: | All GC-MS analysis was performed with an Agilent 5977b GC-MS MSD-HES and an Agilent 7693A automatic liquid sampler. Dried samples were suspended in 40 µL of a 40 mg/mL O-methoxylamine hydrochloride (MOX) (MP Bio #155405) in dry pyridine (EMD Millipore #PX2012-7) and incubated for one hour at 37 °C in a sand bath. 25 µL of this solution was added to auto sampler vials. 60 µL of N-methyl-N-trimethylsilyltrifluoracetamide (MSTFA with 1%TMCS, Thermo #TS48913) was added automatically via the auto sampler and incubated for 30 minutes at 37 °C. After incubation, samples were vortexed and 1 µL of the prepared sample was injected into the gas chromatograph inlet in the split mode with the inlet temperature held at 250°C. A 10:1 split ratio was used for analysis of the majority of metabolites. The gas chromatograph had an initial temperature of 60°C for one minute followed by a 10°C/min ramp to 325°C and a hold time of 5 minutes. A 30-meter Phenomenex Zebron AB-5HT with 5m inert Guardian capillary column was employed for chromatographic separation. Helium was used as the carrier gas at a rate of 1 mL/min. |
| Instrument Name: | Agilent 5977b |
| Column Name: | Phenomenex Zebron AB-5HT (5m) |
| Chromatography Type: | GC |
MS:
| MS ID: | MS002185 |
| Analysis ID: | AN002343 |
| Instrument Name: | Agilent 5977 |
| Instrument Type: | Single quadrupole |
| MS Type: | EI |
| MS Comments: | All GC-MS analysis was performed with an Agilent 5977b GC-MS MSD-HES and an Agilent 7693A automatic liquid sampler. Dried samples were suspended in 40 µL of a 40 mg/mL O-methoxylamine hydrochloride (MOX) (MP Bio #155405) in dry pyridine (EMD Millipore #PX2012-7) and incubated for one hour at 37 °C in a sand bath. 25 µL of this solution was added to auto sampler vials. 60 µL of N-methyl-N-trimethylsilyltrifluoracetamide (MSTFA with 1%TMCS, Thermo #TS48913) was added automatically via the auto sampler and incubated for 30 minutes at 37 °C. After incubation, samples were vortexed and 1 µL of the prepared sample was injected into the gas chromatograph inlet in the split mode with the inlet temperature held at 250°C. A 10:1 split ratio was used for analysis of the majority of metabolites. For those metabolites that saturated the instrument at the 10:1 split concentration, a split of 50:1 was used for analysis. The gas chromatograph had an initial temperature of 60°C for one minute followed by a 10°C/min ramp to 325°C and a hold time of 5 minutes. A 30-meter Phenomenex Zebron AB-5HT with 5m inert Guardian capillary column was employed for chromatographic separation. Helium was used as the carrier gas at a rate of 1 mL/min. Data was collected using MassHunter software (Agilent). Metabolites were identified and their peak area was recorded using MassHunter Quant. This data was transferred to an Excel spread sheet (Microsoft, Redmond WA). Metabolite identity was established using a combination of an in-house metabolite library developed using pure purchased standards, the NIST library and the Fiehn library. |
| Ion Mode: | POSITIVE |
