Summary of Study ST000243

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 PR000196. The data can be accessed directly via it's Project DOI: 10.21228/M82C7Z This work is supported by NIH grant, U2C- DK119886.

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Study IDST000243
Study TitleMetabolomic-based investigation on the effects of antifungal agents in Candida albicans
Study Typein vitro study/drug dosage
Study SummaryOur aim is to determine the metabolic effects of increasing doses of an antifungal agent on C. albicans metabolism (untargeted, steady state metabolomics). We will culture in vitro Candida cells to the mid-logarithmic growth in liquid media (RPMI-1640) at 37°C and then inoculate biological replicates (1ml) onto 22mm nitrocellulose filters under vocuum filtration in sterile conditions. Subsequently, isolates will be cultivated to midlogarithmic phase of growth on the same agar (RPMI-1640) to which the antifungal agent has been added at a range of concentrations to achieve doses equivalent to 0 MIC (no drug), 0.0625 MIC, 0.125 MIC, 0.25 MIC, 0.5 MIC and 1.0 MIC at 37°C. At mid-logarithmic phase of growth (12h) replicates will be metabolically quenched by immersion into a solvent mixture of 40% acetonitrile: 40% methanol: 20% water precooled at -40°C. The resulting quenched isolate/solvent mixtrue will be mechanically lysed by bead-beating with 0.1mm Zirconia beads in a tissue homogenizer and then centrifuged to seperate out cell wall components. Supernatants will be removed and stored at -80°C until they will be sent to SECIM facility.
Institute
University of Florida
DepartmentSECIM
Last NameKatragkou
First NameAspasia
Emailask2012@med.cornell.edu
Submit Date2015-02-10
Num Groups96
Raw Data AvailableYes
Raw Data File Type(s)mzXML
Analysis Type DetailLC-MS
Release Date2016-09-23
Release Version1
Aspasia Katragkou Aspasia Katragkou
https://dx.doi.org/10.21228/M82C7Z
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR000196
Project DOI:doi: 10.21228/M82C7Z
Project Title:Metabolomic-based investigation on the effects of antifungal agents in Candida albicans
Project Summary:Our aim is to determine the metabolic effects of increasing doses of an antifungal agent on C. albicans metabolism (untargeted, steady state metabolomics). We will culture in vitro Candida cells to the mid-logarithmic growth in liquid media (RPMI-1640) at 37°C and then inoculate biological replicates (1ml) onto 22mm nitrocellulose filters under vocuum filtration in sterile conditions. Subsequently, isolates will be cultivated to midlogarithmic phase of growth on the same agar (RPMI-1640) to which the antifungal agent has been added at a range of concentrations to achieve doses equivalent to 0 MIC (no drug), 0.0625 MIC, 0.125 MIC, 0.25 MIC, 0.5 MIC and 1.0 MIC at 37°C. At mid-logarithmic phase of growth (12h) replicates will be metabolically quenched by immersion into a solvent mixture of 40% acetonitrile: 40% methanol: 20% water precooled at -40°C. The resulting quenched isolate/solvent mixtrue will be mechanically lysed by bead-beating with 0.1mm Zirconia beads in a tissue homogenizer and then centrifuged to seperate out cell wall components. Supernatants will be removed and stored at -80°C until they will be sent to SECIM facility.
Institute:Weill Cornell Medicine
Department:Medicine/Infectious Diseases
Last Name:Walsh
First Name:Thomas
Email:thw2003@med.cornell.edu
Funding Source:Southeastern Center for Integrated Metabolomics (SECIM) pilot and feasibility funding, NIH U24 DK097209

Subject:

Subject ID:SU000263
Subject Type:Yeast cells
Subject Species:Candida albicans
Taxonomy ID:5476
Genotype Strain:SC5314
Species Group:Yeast

Factors:

Subject type: Yeast cells; Subject species: Candida albicans (Factor headings shown in green)

mb_sample_id local_sample_id Treatment Experiment
SA011169EXP_1_0.0625MIC_30.0625MIC 1
SA011170EXP_1_0.0625MIC_20.0625MIC 1
SA011171EXP_1_0.0625MIC_40.0625MIC 1
SA011172EXP_1_0.0625MIC_50.0625MIC 1
SA011173EXP_1_0.0625MIC_70.0625MIC 1
SA011174EXP_1_0.0625MIC_60.0625MIC 1
SA011175EXP_1_0.0625MIC_10.0625MIC 1
SA011176EXP_1_0.0625MIC_80.0625MIC 1
SA011177EXP_2_0.0625MIC_80.0625MIC 2
SA011178EXP_2_0.0625MIC_10.0625MIC 2
SA011179EXP_2_0.0625MIC_20.0625MIC 2
SA011180EXP_2_0.0625MIC_60.0625MIC 2
SA011181EXP_2_0.0625MIC_70.0625MIC 2
SA011182EXP_2_0.0625MIC_30.0625MIC 2
SA011183EXP_2_0.0625MIC_40.0625MIC 2
SA011184EXP_2_0.0625MIC_50.0625MIC 2
SA011185EXP_1_0.125MIC_60.125MIC 1
SA011186EXP_1_0.125MIC_80.125MIC 1
SA011187EXP_1_0.125MIC_50.125MIC 1
SA011188EXP_1_0.125MIC_70.125MIC 1
SA011189EXP_1_0.125MIC_40.125MIC 1
SA011190EXP_1_0.125MIC_10.125MIC 1
SA011191EXP_1_0.125MIC_20.125MIC 1
SA011192EXP_1_0.125MIC_30.125MIC 1
SA011193EXP_2_0.125MIC_60.125MIC 2
SA011194EXP_2_0.125MIC_10.125MIC 2
SA011195EXP_2_0.125MIC_50.125MIC 2
SA011196EXP_2_0.125MIC_70.125MIC 2
SA011197EXP_2_0.125MIC_30.125MIC 2
SA011198EXP_2_0.125MIC_80.125MIC 2
SA011199EXP_2_0.125MIC_20.125MIC 2
SA011200EXP_2_0.125MIC_40.125MIC 2
SA011201EXP_1_0.25MIC_80.25MIC 1
SA011202EXP_1_0.25MIC_60.25MIC 1
SA011203EXP_1_0.25MIC_70.25MIC 1
SA011204EXP_1_0.25MIC_40.25MIC 1
SA011205EXP_1_0.25MIC_50.25MIC 1
SA011206EXP_1_0.25MIC_30.25MIC 1
SA011207EXP_1_0.25MIC_20.25MIC 1
SA011208EXP_1_0.25MIC_10.25MIC 1
SA011209EXP_2_0.25MIC_40.25MIC 2
SA011210EXP_2_0.25MIC_30.25MIC 2
SA011211EXP_2_0.25MIC_20.25MIC 2
SA011212EXP_2_0.25MIC_50.25MIC 2
SA011213EXP_2_0.25MIC_10.25MIC 2
SA011214EXP_2_0.25MIC_80.25MIC 2
SA011215EXP_2_0.25MIC_70.25MIC 2
SA011216EXP_2_0.25MIC_60.25MIC 2
SA011217EXP_1_0.5MIC_60.5MIC 1
SA011218EXP_1_0.5MIC_30.5MIC 1
SA011219EXP_1_0.5MIC_70.5MIC 1
SA011220EXP_1_0.5MIC_40.5MIC 1
SA011221EXP_1_0.5MIC_50.5MIC 1
SA011222EXP_1_0.5MIC_80.5MIC 1
SA011223EXP_1_0.5MIC_10.5MIC 1
SA011224EXP_1_0.5MIC_20.5MIC 1
SA011225EXP_2_0.5MIC_60.5MIC 2
SA011226EXP_2_0.5MIC_80.5MIC 2
SA011227EXP_2_0.5MIC_70.5MIC 2
SA011228EXP_2_0.5MIC_50.5MIC 2
SA011229EXP_2_0.5MIC_30.5MIC 2
SA011230EXP_2_0.5MIC_10.5MIC 2
SA011231EXP_2_0.5MIC_20.5MIC 2
SA011232EXP_2_0.5MIC_40.5MIC 2
SA011233EXP_1_1.0MIC_81.0MIC 1
SA011234EXP_1_1.0MIC_51.0MIC 1
SA011235EXP_1_1.0MIC_61.0MIC 1
SA011236EXP_1_1.0MIC_41.0MIC 1
SA011237EXP_1_1.0MIC_31.0MIC 1
SA011238EXP_1_1.0MIC_21.0MIC 1
SA011239EXP_1_1.0MIC_71.0MIC 1
SA011240EXP_1_1.0MIC_11.0MIC 1
SA011241EXP_2_1.0MIC_31.0MIC 2
SA011242EXP_2_1.0MIC_21.0MIC 2
SA011243EXP_2_1.0MIC_11.0MIC 2
SA011244EXP_2_1.0MIC_51.0MIC 2
SA011245EXP_2_1.0MIC_41.0MIC 2
SA011246EXP_2_1.0MIC_71.0MIC 2
SA011247EXP_2_1.0MIC_81.0MIC 2
SA011248EXP_2_1.0MIC_61.0MIC 2
SA011249EXP_1_0MIC_4no drug 1
SA011250EXP_1_0MIC_3no drug 1
SA011251EXP_1_0MIC_2no drug 1
SA011252EXP_1_0MIC_5no drug 1
SA011253EXP_1_0MIC_6no drug 1
SA011254EXP_1_0MIC_1no drug 1
SA011255EXP_1_0MIC_8no drug 1
SA011256EXP_1_0MIC_7no drug 1
SA011257EXP_2_0MIC_3no drug 2
SA011258EXP_2_0MIC_2no drug 2
SA011259EXP_2_0MIC_4no drug 2
SA011260EXP_2_0MIC_6no drug 2
SA011261EXP_2_0MIC_8no drug 2
SA011262EXP_2_0MIC_7no drug 2
SA011263EXP_2_0MIC_1no drug 2
SA011264EXP_2_0MIC_5no drug 2
Showing results 1 to 96 of 96

Collection:

Collection ID:CO000254
Collection Summary:Culture supernatants (appx. 1 ml from each replicate) will be removed and stored at -80C
Sample Type:Cells
Volumeoramount Collected:1 mL
Storage Conditions:-80C

Treatment:

Treatment ID:TR000274
Treatment Summary:Candida cells grown to the mid-logarithmic phase will be exposed in biological replicates (X8) to the antifungal agent (micafungin) to a range of concentrations (sub-concentrations of the strain's MIC, Minimal Inhibitory Concentration) 0.0625MIC 0.125MIC 0.25MIC 0.5MIC
1.0MIC. No drug exposed Candida cells will serve as controls

Sample Preparation:

Sampleprep ID:SP000268
Sampleprep Summary:-
Sampleprep Protocol Filename:Sample_Preparation_of_Cell_Lysates.pdf

Combined analysis:

Analysis ID AN000379 AN000380
Analysis type MS MS
Chromatography type Reversed phase Reversed phase
Chromatography system Thermo Dionex Ultimate 3000 Thermo Dionex Ultimate 3000
Column ACE Excel 2 C18-PFP (100 x 2.1mm, 2um) ACE Excel 2 C18-PFP (100 x 2.1mm, 2um)
MS Type ESI ESI
MS instrument type Orbitrap Orbitrap
MS instrument name Thermo Q Exactive Orbitrap Thermo Q Exactive Orbitrap
Ion Mode POSITIVE NEGATIVE
Units Peak height Peak height

Chromatography:

Chromatography ID:CH000273
Methods Filename:Metabolomics_LCMSProtocol.pdf
Appendix_A_-_Internal_Standard_Prep_GLCMS.pdf
Instrument Name:Thermo Dionex Ultimate 3000
Column Name:ACE Excel 2 C18-PFP (100 x 2.1mm, 2um)
Flow Rate:0.350mL/min-0.600mL/min
Internal Standard:Appendix A - Internal Standard Prep GLCMS.pdf
Solvent A:100% water; 0.1% formic acid
Solvent B:100% acetonitrile
Chromatography Type:Reversed phase

MS:

MS ID:MS000325
Analysis ID:AN000379
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
Ion Mode:POSITIVE
  
MS ID:MS000326
Analysis ID:AN000380
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
Ion Mode:NEGATIVE
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