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

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Study IDST001401
Study TitleSteady-state metabolomics time course of Saccharomyces cerevisiae mitochondrial fatty acid synthesis (mtFAS) mutants
Study TypeSteady-state targeted and untargeted metabolomics time course
Study SummaryThe 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
DepartmentBiochemistry
LaboratoryRutter
Last NameBerg
First NameJordan
Address15 N Medical Drive East RM 5520, Salt Lake City, UT 84112-5650 USA
Emailjordan.berg@biochem.utah.edu
Phone(801) 581 3340
Submit Date2020-06-10
Num Groups3
Total Subjects95
Raw Data AvailableYes
Raw Data File Type(s).xml;csv;bin
Analysis Type DetailGC-MS
Release Date2020-06-22
Release Version1
Jordan Berg Jordan Berg
https://dx.doi.org/10.21228/M8GD71
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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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
SA113818mct1KO at 0hr minR+Leu Sample5mct1_KO minR+Leu 0 min
SA113819mct1KO at 0hr minR+Leu Sample3mct1_KO minR+Leu 0 min
SA113820mct1KO at 0hr minR+Leu Sample4mct1_KO minR+Leu 0 min
SA113821mct1KO at 0hr minR+Leu Sample1mct1_KO minR+Leu 0 min
SA113822mct1KO at 0hr minR+Leu Sample2mct1_KO minR+Leu 0 min
SA113823mct1KO at 0hr minR+Leu Sample6mct1_KO minR+Leu 0 min
SA113824mct1KO at 15min minR+Leu Sample2mct1_KO minR+Leu 15min
SA113825mct1KO at 15min minR+Leu Sample5mct1_KO minR+Leu 15min
SA113826mct1KO at 15min minR+Leu Sample6mct1_KO minR+Leu 15min
SA113827mct1KO at 15min minR+Leu Sample4mct1_KO minR+Leu 15min
SA113828mct1KO at 15min minR+Leu Sample3mct1_KO minR+Leu 15min
SA113829mct1KO at 15min minR+Leu Sample1mct1_KO minR+Leu 15min
SA113830mct1KO at 3hr minR+Leu Sample1mct1_KO minR+Leu 180 min
SA113831mct1KO at 3hr minR+Leu Sample2mct1_KO minR+Leu 180 min
SA113832mct1KO at 3hr minR+Leu Sample3mct1_KO minR+Leu 180 min
SA113833mct1KO at 3hr minR+Leu Sample5mct1_KO minR+Leu 180 min
SA113834mct1KO at 3hr minR+Leu Sample4mct1_KO minR+Leu 180 min
SA113835mct1KO at 3hr minR+Leu Sample6mct1_KO minR+Leu 180 min
SA113836mct1KO at 30min minR+Leu Sample5mct1_KO minR+Leu 30 min
SA113837mct1KO at 30min minR+Leu Sample2mct1_KO minR+Leu 30 min
SA113838mct1KO at 30min minR+Leu Sample4mct1_KO minR+Leu 30 min
SA113839mct1KO at 30min minR+Leu Sample6mct1_KO minR+Leu 30 min
SA113840mct1KO at 30min minR+Leu Sample3mct1_KO minR+Leu 30 min
SA113841mct1KO at 30min minR+Leu Sample1mct1_KO minR+Leu 30 min
SA113842mct1KO at 1hr minR+Leu Sample6mct1_KO minR+Leu 60 min
SA113843mct1KO at 1hr minR+Leu Sample5mct1_KO minR+Leu 60 min
SA113844mct1KO at 1hr minR+Leu Sample3mct1_KO minR+Leu 60 min
SA113845mct1KO at 1hr minR+Leu Sample4mct1_KO minR+Leu 60 min
SA113846mct1KO at 1hr minR+Leu Sample1mct1_KO minR+Leu 60 min
SA113847mct1KO at 1hr minR+Leu Sample2mct1_KO minR+Leu 60 min
SA113848oar1 KO at 0hr minR+Leu Sample5oar1_KO minR+Leu 0 min
SA113849oar1 KO at 0hr minR+Leu Sample6oar1_KO minR+Leu 0 min
SA113850oar1 KO at 0hr minR+Leu Sample4oar1_KO minR+Leu 0 min
SA113851oar1 KO at 0hr minR+Leu Sample3oar1_KO minR+Leu 0 min
SA113852oar1 KO at 0hr minR+Leu Sample2oar1_KO minR+Leu 0 min
SA113853oar1 KO at 0hr minR+Leu Sample1oar1_KO minR+Leu 0 min
SA113854oar1 KO at 15min minR+Leu Sample1oar1_KO minR+Leu 15min
SA113855oar1 KO at 15min minR+Leu Sample4oar1_KO minR+Leu 15min
SA113856oar1 KO at 15min minR+Leu Sample2oar1_KO minR+Leu 15min
SA113857oar1 KO at 15min minR+Leu Sample5oar1_KO minR+Leu 15min
SA113858oar1 KO at 15min minR+Leu Sample3oar1_KO minR+Leu 15min
SA113859oar1 KO at 15min minR+Leu Sample6oar1_KO minR+Leu 15min
SA113860oar1 KO at 3hr minR+Leu Sample5oar1_KO minR+Leu 180 min
SA113861oar1 KO at 3hr minR+Leu Sample6oar1_KO minR+Leu 180 min
SA113862oar1 KO at 3hr minR+Leu Sample4oar1_KO minR+Leu 180 min
SA113863oar1 KO at 3hr minR+Leu Sample3oar1_KO minR+Leu 180 min
SA113864oar1 KO at 3hr minR+Leu Sample1oar1_KO minR+Leu 180 min
SA113865oar1 KO at 3hr minR+Leu Sample2oar1_KO minR+Leu 180 min
SA113866oar1 KO at 30min minR+Leu Sample6oar1_KO minR+Leu 30 min
SA113867oar1 KO at 30min minR+Leu Sample2oar1_KO minR+Leu 30 min
SA113868oar1 KO at 30min minR+Leu Sample3oar1_KO minR+Leu 30 min
SA113869oar1 KO at 30min minR+Leu Sample1oar1_KO minR+Leu 30 min
SA113870oar1 KO at 30min minR+Leu Sample4oar1_KO minR+Leu 30 min
SA113871oar1 KO at 30min minR+Leu Sample5oar1_KO minR+Leu 30 min
SA113872oar1 KO at 1hr minR+Leu Sample2oar1_KO minR+Leu 60 min
SA113873oar1 KO at 1hr minR+Leu Sample3oar1_KO minR+Leu 60 min
SA113874oar1 KO at 1hr minR+Leu Sample6oar1_KO minR+Leu 60 min
SA113875oar1 KO at 1hr minR+Leu Sample1oar1_KO minR+Leu 60 min
SA113876oar1 KO at 1hr minR+Leu Sample4oar1_KO minR+Leu 60 min
SA113877oar1 KO at 1hr minR+Leu Sample5oar1_KO minR+Leu 60 min
SA113878PB Sample1pb - -
SA113879PB Sample2pb - -
SA113880PB Sample3pb - -
SA113881QC Sample3qc - -
SA113882QC Sample2qc - -
SA113883QC Sample1qc - -
SA113884WT at 0hr minR+Leu Sample6wild-type minR+Leu 0 min
SA113885WT at 0hr minR+Leu Sample1wild-type minR+Leu 0 min
SA113886WT at 0hr minR+Leu Sample5wild-type minR+Leu 0 min
SA113887WT at 0hr minR+Leu Sample3wild-type minR+Leu 0 min
SA113888WT at 0hr minR+Leu Sample4wild-type minR+Leu 0 min
SA113889WT at 0hr minR+Leu Sample2wild-type minR+Leu 0 min
SA113890WT at 15min minR+Leu Sample4wild-type minR+Leu 15min
SA113891WT at 15min minR+Leu Sample5wild-type minR+Leu 15min
SA113892WT at 15min minR+Leu Sample3wild-type minR+Leu 15min
SA113893WT at 15min minR+Leu Sample1wild-type minR+Leu 15min
SA113894WT at 15min minR+Leu Sample6wild-type minR+Leu 15min
SA113895WT at 15min minR+Leu Sample2wild-type minR+Leu 15min
SA113896WT at 3hr minR+Leu Sample1wild-type minR+Leu 180 min
SA113897WT at 3hr minR+Leu Sample2wild-type minR+Leu 180 min
SA113898WT at 3hr minR+Leu Sample3wild-type minR+Leu 180 min
SA113899WT at 3hr minR+Leu Sample4wild-type minR+Leu 180 min
SA113900WT at 3hr minR+Leu Sample5wild-type minR+Leu 180 min
SA113901WT at 30min minR+Leu Sample5wild-type minR+Leu 30 min
SA113902WT at 30min minR+Leu Sample6wild-type minR+Leu 30 min
SA113903WT at 30min minR+Leu Sample1wild-type minR+Leu 30 min
SA113904WT at 30min minR+Leu Sample4wild-type minR+Leu 30 min
SA113905WT at 30min minR+Leu Sample3wild-type minR+Leu 30 min
SA113906WT at 30min minR+Leu Sample2wild-type minR+Leu 30 min
SA113907WT at 1hr minR+Leu Sample2wild-type minR+Leu 60 min
SA113908WT at 1hr minR+Leu Sample1wild-type minR+Leu 60 min
SA113909WT at 1hr minR+Leu Sample3wild-type minR+Leu 60 min
SA113910WT at 1hr minR+Leu Sample5wild-type minR+Leu 60 min
SA113911WT at 1hr minR+Leu Sample6wild-type minR+Leu 60 min
SA113912WT at 1hr minR+Leu Sample4wild-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 HES-MSD
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:HES-MSD
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
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