Summary of study ST000569

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 PR000417. The data can be accessed directly via it's Project DOI: 10.21228/M8531V This work is supported by NIH grant, U2C- DK119886.

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Study IDST000569
Study TitleEffect of minimal and complex media on the metabolite profiles
Study SummaryMedia dependent intracellular metabolite changes of microorganisms
Institute
Graduate school of Korea University
Last NameKim
First NameJungyeon
Address145, Anam-ro, Seongbuk-gu, Seoul, Seoul, 02841, Korea, South
Emailkim131812@korea.ac.kr
Phone821082248015
Submit Date2017-03-07
Study CommentsEach class means,Intracellular metabolites of E.coli cultivated in M9 Intracellular metabolites of E.coli cultivated in LB Intracellular metabolites of S.cerevisiae cultivated in YNB Intracellular metabolites of S.cerevisiae cultivated in YPD.
Raw Data AvailableYes
Raw Data File Type(s).peg
Analysis Type DetailGC-MS
Release Date2017-07-10
Release Version1
Jungyeon Kim Jungyeon Kim
https://dx.doi.org/10.21228/M8531V
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR000417
Project DOI:doi: 10.21228/M8531V
Project Title:Effect of media on metabolite profiles of E coli and Saccharomyces cerevisiae
Project Type:Media Process Biochemistry
Project Summary:Effect of minimal and complex media on the metabolite profiles of Escherichia coli and Saccharomyces cerevisiae
Institute:Graduate school of Korea University
Last Name:Kim
First Name:Jungyeon
Address:145, Anam-ro, Seongbuk-gu, Seoul, Seoul, 02841, Korea, South
Email:kim131812@korea.ac.kr
Phone:821082248015

Subject:

Subject ID:SU000591
Subject Type:Microorganisms
Subject Species:Saccharomyces cerevisiae
Taxonomy ID:4932
Species Group:Microorganism

Factors:

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

mb_sample_id local_sample_id treatment
SA029901140505aaasa09_1Media - LB
SA029902140505aaasa15_1Media - LB
SA029903140505aaasa13_1Media - LB
SA029904140505aaasa10_1Media - LB
SA029905140505aaasa11_1Media - LB
SA029906140505aaasa12_1Media - LB
SA029907140505aaasa08_1Media - M9
SA029908140505aaasa04_1Media - M9
SA029909140505aaasa02_1Media - M9
SA029910140505aaasa03_1Media - M9
SA029911140505aaasa07_1Media - M9
SA029912140505aaasa01_1Media - M9
SA029913140328aaasa19_1Media - YNB
SA029914140328aaasa08_1Media - YNB
SA029915140328aaasa04_1Media - YNB
SA029916140328aaasa11_1Media - YNB
SA029917140328aaasa18_1Media - YNB
SA029918140328aaasa13_1Media - YNB
SA029919140328aaasa21_1Media - YPD
SA029920140328aaasa17_1Media - YPD
SA029921140328aaasa12_1Media - YPD
SA029922140328aaasa09_1Media - YPD
SA029923140328aaasa10_1Media - YPD
SA029924140328aaasa14_1Media - YPD
Showing results 1 to 24 of 24

Collection:

Collection ID:CO000585
Collection Summary:Fast filtration: cells for each experimental condition were obtained by filtering 1 ml of the cell culture using a nylon membrane filter (0.45-µm pore size, Whatman, Piscataway, NJ) under vacuum. Then, the cell mass was washed with 5 ml of distilled water at room temperature. The cells on the membrane filter were quenched in 10 ml of acetonitrile/water (1:1, v/v) extraction solvent at −20 °C.
Sample Type:Bacterial cells

Treatment:

Treatment ID:TR000605
Treatment Summary:E. coli MG1655 was cultivated in a 100-ml working volume in 250 ml flasks at 37 °C, with shaking at 200 rpm. The culture media for E. coli MG1655 were minimal M9 medium (Difco Laboratories, Detroit, MI) and complex Luria broth (Difco Laboratories). S. cerevisiae BY4741 was cultivated in a 100-ml working volume in 250 ml flasks at 30 °C, with shaking at 200 rpm. The culture media were a minimal medium of the yeast nitrogen base broth (Difco Laboratories) and a complex medium of YP broth (Difco Laboratories). All media contained 2% (w/v) glucose as a sole carbon source.

Sample Preparation:

Sampleprep ID:SP000598
Sampleprep Summary:metabolite samples were derivatized in two steps. First, the samples were incubated with 5 µl of 40 mg/ml methoxyamine hydrochloride in pyridine (Sigma-Aldrich, St. Louis, MO) at 30 °C for 90 min, and then, with 45 µl of N-methyl-N-trimethylsilyl-trifluoroacetamide (Fluka, Buchs, Switzerland) at 37 °C for 30 min. A mixture of fatty acid methyl esters including methyl forms of C8, C9, C10, C12, C14, C16, C18, C20, C22, C24, C26, C28, and C30 was added to the derivatized sample as the retention index markers.

Combined analysis:

Analysis ID AN000876
Analysis type MS
Chromatography type GC
Chromatography system Agilent 7890B
Column RTX-5Sil MS column
MS Type EI
MS instrument type GC-TOF
MS instrument name Leco Pegasus HT TOF
Ion Mode POSITIVE
Units Intensity

Chromatography:

Chromatography ID:CH000622
Chromatography Summary:An aliquot of 0.5 µl of the derivatized sample was injected into the GC, in splitless mode, and separated on an RTX-5Sil MS column (30-m length, 0.25-mm inner diameter, and 0.25-µm film thickness; Restek, Bellefonte, PA) with an additional 10-m guard column. The oven temperature was initially set at 50 °C for 1 min, then ramped to 330 °C at a rate of 20 °C/min, and held at 330 °C for 5 min.
Instrument Name:Agilent 7890B
Column Name:RTX-5Sil MS column
Chromatography Type:GC

MS:

MS ID:MS000777
Analysis ID:AN000876
Instrument Name:Leco Pegasus HT TOF
Instrument Type:GC-TOF
MS Type:EI
Ion Mode:POSITIVE
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