Summary of study ST001612

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 PR001034. The data can be accessed directly via it's Project DOI: 10.21228/M81X28 This work is supported by NIH grant, U2C- DK119886.

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Study IDST001612
Study TitleComparative metabolomics analysis of two Saccharomyces cerevisiae strains: the wild type and mtl1Δ, which carries a deletion of the mechanosensor Mtl1p (part-II)
Study SummaryTo gather more in-depth knowledge of the Mtl1p mechanosensor's role in Saccharomyces cerevisiae metabolism, we conducted a comparative metabolomic analysis of two Saccharomyces cerevisiae strains: the wild type and mtl1Δ, which carries a deletion of the mechanosensor Mtl1p. Both strains were grown under normal conditions at 27°C. The most significant metabolic changes between these strains were related to amino acid metabolism, purine metabolism, and carboxylic acid metabolism.
Institute
University of Puerto Rico, Medical Sciences Campus
DepartmentBiochemistry
Last NameChorna
First NameNataliya
AddressUniversity of Puerto Rico, Medical Sciences Campus, Department of Biochemistry, Main Building, 6th Floor, Room A-632, San Juan, PR 00935
Emailnataliya.chorna@upr.edu
Phone7877582525 ext 1640
Submit Date2020-11-07
Num Groups2
Total Subjects14
Raw Data AvailableYes
Raw Data File Type(s)qgd
Analysis Type DetailGC-MS
Release Date2020-12-10
Release Version1
Nataliya Chorna Nataliya Chorna
https://dx.doi.org/10.21228/M81X28
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR001034
Project DOI:doi: 10.21228/M81X28
Project Title:Comparative metabolomics analysis of two Saccharomyces cerevisiae strains: the wild type and mtl1?, which carries a deletion of the mechanosensor Mtl1p
Project Summary:To gather more in-depth knowledge of the Mtl1p mechanosensor's role in Saccharomyces cerevisiae metabolism, we conducted a comparative metabolomic analysis of two Saccharomyces cerevisiae strains: the wild type and mtl1?, which carries a deletion of the mechanosensor Mtl1p. Both strains were grown under normal conditions at 27°C. The most significant metabolic changes between these strains were related to amino acid metabolism, purine metabolism, and carboxylic acid metabolism.
Institute:University of Puerto Rico, Medical Sciences Campus
Department:Biochemistry
Last Name:Chorna
First Name:Nataliya
Address:University of Puerto Rico, Medical Sciences Campus, Department of Biochemistry, Main Building, 6th Floor, Room A-632, San Juan, PR 00935
Email:nataliya.chorna@upr.edu
Phone:787-758-2525 x 1640
Funding Source:NIGMS-NIH-PRINBRE-P20GM103475
Contributors:Nelson Martínez–Matías, Sahily González–Crespo

Subject:

Subject ID:SU001689
Subject Type:Yeast
Subject Species:Saccharomyces cerevisiae
Taxonomy ID:4932
Genotype Strain:BY4742, YGR023w
Cell Biosource Or Supplier:Open Biosystems

Factors:

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

mb_sample_id local_sample_id Strain
SA136783YGR023w-6mtl1Δ
SA136784YGR023w-7mtl1Δ
SA136785YGR023w-5mtl1Δ
SA136786YGR023w-1mtl1Δ
SA136787YGR023w-2mtl1Δ
SA136788YGR023w-3mtl1Δ
SA136789YGR023w-4mtl1Δ
SA136776BY4742-7Wild-type
SA136777BY4742-1Wild-type
SA136778BY4742-5Wild-type
SA136779BY4742-6Wild-type
SA136780BY4742-2Wild-type
SA136781BY4742-3Wild-type
SA136782BY4742-4Wild-type
Showing results 1 to 14 of 14

Collection:

Collection ID:CO001682
Collection Summary:Cells were grown at 27°C, 210 rpm in 5 mL of complete synthetic medium (CSM, 0.67% Nitrogen base without amino acids and ammonium sulfate, 2% glucose). The next day, cells were replaced with fresh CSM and grow at 27°C to reach an OD of 0.6 - 0.7. 25 ml of each sample were harvested by centrifugation at 3,838 x g for 5 min at 4°C, washed with 1 ml ice cold sterile water, quenched using ice cold methanol, and stored at -80°C.
Sample Type:Yeast cells

Treatment:

Treatment ID:TR001702
Treatment Summary:No treatment

Sample Preparation:

Sampleprep ID:SP001695
Sampleprep Summary:Extraction of metabolites was performed by homogenization in 1 mL of cold methanol/H2O (1:1) extraction solution and centrifugated at 167 x g at 4°C for 5 min. Supernatants were collected and evaporated to dryness in a nitrogen stream stream at 50 ºC (RapidVap, Labconco), and derivatized by methoxyamination by adding 50 μl of 20 mg/ml solution of methoxyamine hydrochloride in pyridine followed by incubation at 37°C for 2 hours. Trimethylsilylation was subsequently performed by adding 50 µl of N-methyl-N-trimethylsilyl-trifluoroacetamide (MSTFA+1% TMCS) and incubated for 1 hour at 65°C. Samples were centrifuged at 13000 rpm for 10 minutes at RT. Supernatants were transferred to glass vials for GC/MS analysis

Combined analysis:

Analysis ID AN002647
Analysis type MS
Chromatography type GC
Chromatography system Shimadzu GCMS-QP2010 ultra
Column Shimadzu SH-Rxi-5ms (30 x 0.25 x 0.25)
MS Type EI
MS instrument type Single quadrupole
MS instrument name Shimadzu QP2010 Ultra
Ion Mode POSITIVE
Units mM

Chromatography:

Chromatography ID:CH001955
Instrument Name:Shimadzu GCMS-QP2010 ultra
Column Name:Shimadzu SH-Rxi-5ms (30 x 0.25 x 0.25)
Internal Standard:1 mM 2-Fluobiphenyl
Chromatography Type:GC

MS:

MS ID:MS002459
Analysis ID:AN002647
Instrument Name:Shimadzu QP2010 Ultra
Instrument Type:Single quadrupole
MS Type:EI
MS Comments:Inlet temperature was 280 °C; ion source temperature was 200 °C. MS conditions were set as follows: full scan mode, electron energy of 70 eV, quadrupole scan range of m/z 35–700. Data were processed using the GCMS Solution Postrun Analysis software (Shimadzu Inc) for metabolites identification from their electron impact mass spectra by comparison to the NIST 2014 spectral mass library.
Ion Mode:POSITIVE
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