Summary of Study ST000870

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 IDST000870
Study TitleUntargeted metabolomic profile of Saccharomyces cerevisiae (F2) hybrids (part II)
Study SummaryMetabolomic profiles were compiled from oak and wine yeast parents, and their F2 hybrids. 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

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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:SU000907
Subject Type:Fungal
Subject Species:Saccharomyces cerevisiae
Taxonomy ID:4932
Genotype Strain:BC233, BC240,147 individual BC240/BC233 F2 hybrid segregants
Species Group:Microorganism

Factors:

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

mb_sample_id local_sample_id Parent
SA049734STD_6dBC233_BC240_mix
SA049735STD_7BC233_BC240_mix
SA049736STD_7bBC233_BC240_mix
SA049737STD_6bBC233_BC240_mix
SA049738STD_5BC233_BC240_mix
SA049739STD_6BC233_BC240_mix
SA049740STD_7cBC233_BC240_mix
SA049741STD_6cBC233_BC240_mix
SA049742STD_8BC233_BC240_mix
SA049743STD_8bBC233_BC240_mix
SA049744STD_8cBC233_BC240_mix
SA0497286BC233(YPS606)
SA0497297BC233(YPS606)
SA04973011BC233(YPS606)
SA04973110BC233(YPS606)
SA0497322BC233(YPS606)
SA0497333BC233(YPS606)
SA0497455BC240(UCD2120)
SA0497461BC240(UCD2120)
SA0497478BC240(UCD2120)
SA0497484BC240(UCD2120)
SA0497499BC240(UCD2120)
SA04975012BC240(UCD2120)
SA049751126F2_2A1
SA04975265F2_2A1
SA04975328F2_2A1
SA049754134F2_2A10
SA049755256F2_2A10
SA049756261F2_2A10
SA049757284F2_2A11
SA049758262F2_2A11
SA049759257F2_2A11
SA04976033F2_2A11
SA049761199F2_2A12
SA04976279F2_2A12
SA04976366F2_2A3
SA049764127F2_2A3
SA049765266F2_2A4
SA04976667F2_2A4
SA049767128F2_2A4
SA049768129F2_2A5
SA049769267F2_2A5
SA049770254F2_2A5
SA04977168F2_2A6
SA049772130F2_2A6
SA04977329F2_2A6
SA049774131F2_2A7
SA049775255F2_2A7
SA04977630F2_2A7
SA049777260F2_2A7
SA04977869F2_2A8
SA04977931F2_2A8
SA049780132F2_2A8
SA049781133F2_2A9
SA04978270F2_2A9
SA04978332F2_2A9
SA049784272F2_2B1
SA04978534F2_2B1
SA04978680F2_2B1
SA049787258F2_2B1
SA04978886F2_2B10
SA049789268F2_2B10
SA049790206F2_2B10
SA04979138F2_2B11
SA049792269F2_2B11
SA049793207F2_2B11
SA049794259F2_2B3
SA04979581F2_2B3
SA049796200F2_2B3
SA04979735F2_2B4
SA049798201F2_2B4
SA04979982F2_2B4
SA04980083F2_2B5
SA049801202F2_2B5
SA049802263F2_2B5
SA04980336F2_2B6
SA049804203F2_2B6
SA04980584F2_2B6
SA04980685F2_2B8
SA049807264F2_2B8
SA049808204F2_2B8
SA04980937F2_2B9
SA049810265F2_2B9
SA049811205F2_2B9
SA04981287F2_2C1
SA049813208F2_2C1
SA04981439F2_2C1
SA04981593F2_2C11
SA049816215F2_2C11
SA04981744F2_2C11
SA049818275F2_2C12
SA049819216F2_2C12
SA04982094F2_2C12
SA049821209F2_2C2
SA049822270F2_2C2
SA049823285F2_2C2
SA049824271F2_2C3
SA04982588F2_2C3
SA049826210F2_2C3
SA04982740F2_2C4
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Collection:

Collection ID:CO000901
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:TR000921
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:SP000914
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 AN001417
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:CH000991
Instrument Name:None
Column Name:none
Chromatography Type:None (Direct infusion)

MS:

MS ID:MS001307
Analysis ID:AN001417
Instrument Name:Thermo LTQ Discovery Orbitrap
Instrument Type:Orbitrap
MS Type:API
Ion Mode:NEGATIVE
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