Summary of Study ST000868

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 PR000603. The data can be accessed directly via it's Project DOI: 10.21228/M8QQ3S 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.

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Study IDST000868
Study TitleUntargeted metabolomic profile of oak and wine yeast strains
Study SummaryMetabolomic profiles were compiled from oak and wine yeast parents over three extraction times (batch). Included in this study are extraction controls.
Institute
Washington University in St. Louis
Last NameSwain Lenz
First NameDevjanee
Address4515 McKinley Avenue, Saint Louis, Missouri, 63110, USA
Emaildevjanee.swain.lenz@duke.edu
Phone314-362-3679
Submit Date2017-08-22
Raw Data AvailableYes
Raw Data File Type(s)raw(Thermo)
Analysis Type DetailAPI-MS
Release Date2017-11-20
Release Version1
Devjanee Swain Lenz Devjanee Swain Lenz
https://dx.doi.org/10.21228/M8QQ3S
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR000603
Project DOI:doi: 10.21228/M8QQ3S
Project Title:Causal genetic variation underlying metabolome differences
Project Summary:A goal of biology is to predict the phenotypes of individuals, such as side effects to drugs, from their genotypes. Genetic variants that cause disease can change an individual’s total metabolite profile, or metabolome. Understanding the function of these genetic variants may help predict novel phenotypes. We used an unbiased method in yeast to show that genetic differences in two genes change the levels of several urea cycle metabolites. Leveraging knowledge of the urea cycle, we then predicted and validated the sensitivity of yeast strains to a particular drug. The interpretability of our results demonstrates the promise of using genetic variants underlying differences in the metabolome to predict novel phenotypes from genotype.
Institute:Washington University in St. Louis
Last Name:Swain Lenz
First Name:Devjanee
Address:4515 McKinley Avenue, Saint Louis, Missouri, 63110, USA
Email:devjanee.swain.lenz@duke.edu
Phone:314-362-3679

Subject:

Subject ID:SU000906
Subject Type:Fungal
Subject Species:Saccharomyces cerevisiae
Taxonomy ID:4932
Genotype Strain:BC233, BC240
Species Group:Microorganism

Factors:

Subject type: Fungal; Subject species: Saccharomyces cerevisiae (Factor headings shown in green)

mb_sample_id local_sample_id Parent
SA0496772015_10_27_KBC233(YPS606)
SA0496782015_04_08_DBC233(YPS606)
SA0496792015_03_21_JBC233(YPS606)
SA0496802015_10_30_BBC233(YPS606)
SA0496812015_11_11_FBC233(YPS606)
SA0496822015_11_16_BBC233(YPS606)
SA0496832015_11_14_EBC233(YPS606)
SA04968411BC233(YPS606)
SA0496852015_11_02_ABC233(YPS606)
SA0496862015_03_21_BBC233(YPS606)
SA0496876BC233(YPS606)
SA0496887BC233(YPS606)
SA04968910BC233(YPS606)
SA0496902BC233(YPS606)
SA0496913BC233(YPS606)
SA0496922015_04_08_JBC240(UCD2120)
SA0496939BC240(UCD2120)
SA0496942015_04_07_BBC240(UCD2120)
SA0496952015_11_02_DBC240(UCD2120)
SA0496962015_10_30_DBC240(UCD2120)
SA0496972015_10_28_GBC240(UCD2120)
SA0496988BC240(UCD2120)
SA0496992015_04_15_HBC240(UCD2120)
SA04970012BC240(UCD2120)
SA0497012015_11_11_EBC240(UCD2120)
SA0497021BC240(UCD2120)
SA0497034BC240(UCD2120)
SA0497042015_11_13_SBC240(UCD2120)
SA0497055BC240(UCD2120)
SA0497062015_11_16_NBC240(UCD2120)
SA04970715media only
SA04970819media only
SA04970917media only
SA04971021media only
SA04971125media only
SA04971223media only
SA0497132015_10_28_Nno cells/no media
SA0497142015_10_30_Nno cells/no media
SA0497152015_04_14_Pno cells/no media
SA04971620no cells/no media
SA04971722no cells/no media
SA04971818no cells/no media
SA04971916no cells/no media
SA04972014no cells/no media
SA04972124no cells/no media
SA04972226no cells/no media
SA0497232015_04_22_Fno cells/no media
SA0497242015_04_21_Pno cells/no media
SA0497252015_04_15_Pno cells/no media
SA0497262015_04_13_Pno cells/no media
SA0497272015_10_27_Nno cells/no media
Showing results 1 to 51 of 51

Collection:

Collection ID:CO000900
Collection Summary:Cells were grown at 30°C in synthetic dextrose media (0.145% yeast nitrogen base minus amino acids/ammonium sulfate, 0.5% ammonium sulfate, 2% dextrose) to an OD of 0.55 - 0.65. We harvested cells by vacuum filter.
Sample Type:Yeast cells

Treatment:

Treatment ID:TR000920
Treatment Summary:Cells were grown at 30°C in synthetic dextrose media (0.145% yeast nitrogen base minus amino acids/ammonium sulfate, 0.5% ammonium sulfate, 2% dextrose) to an OD of 0.55 - 0.65. Different genotypes were used, and media was made at three separate times (batch).

Sample Preparation:

Sampleprep ID:SP000913
Sampleprep Summary:We harvested cells by vacuum filter, and extracted hydrophilic metabolites from 0.2 um filters using 40:40:20% (v/v/v) methanol/acetonitrile/water8. We froze and thawed extracts at -80 °C and -20 °C, respectively, three times. We pelleted cells, and stored the supernatant at -80 °C until we performed mass spectrometry

Combined analysis:

Analysis ID AN001416
Analysis type MS
Chromatography type None (Direct infusion)
Chromatography system None
Column none
MS Type API
MS instrument type Orbitrap
MS instrument name Thermo LTQ Discovery Orbitrap
Ion Mode NEGATIVE
Units normalized peak intensity

Chromatography:

Chromatography ID:CH000990
Instrument Name:None
Column Name:none
Chromatography Type:None (Direct infusion)

MS:

MS ID:MS001306
Analysis ID:AN001416
Instrument Name:Thermo LTQ Discovery Orbitrap
Instrument Type:Orbitrap
MS Type:API
Ion Mode:NEGATIVE
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