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.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
| Study ID | ST001612 |
| Study Title | Comparative metabolomics analysis of two Saccharomyces cerevisiae strains: the wild type and mtl1Δ, which carries a deletion of the mechanosensor Mtl1p (part-II) |
| Study 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 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 |
| 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 |
| nataliya.chorna@upr.edu | |
| Phone | 7877582525 ext 1640 |
| Submit Date | 2020-11-07 |
| Num Groups | 2 |
| Total Subjects | 14 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | qgd |
| Analysis Type Detail | GC-MS |
| Release Date | 2020-12-10 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
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 |
|---|---|---|
| SA136783 | YGR023w-6 | mtl1Δ |
| SA136784 | YGR023w-7 | mtl1Δ |
| SA136785 | YGR023w-5 | mtl1Δ |
| SA136786 | YGR023w-1 | mtl1Δ |
| SA136787 | YGR023w-2 | mtl1Δ |
| SA136788 | YGR023w-3 | mtl1Δ |
| SA136789 | YGR023w-4 | mtl1Δ |
| SA136776 | BY4742-7 | Wild-type |
| SA136777 | BY4742-1 | Wild-type |
| SA136778 | BY4742-5 | Wild-type |
| SA136779 | BY4742-6 | Wild-type |
| SA136780 | BY4742-2 | Wild-type |
| SA136781 | BY4742-3 | Wild-type |
| SA136782 | BY4742-4 | Wild-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 (30m x 0.25mm,0.25um) |
| 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 (30m x 0.25mm,0.25um) |
| 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 |
