Summary of Study ST000466
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 PR000358. The data can be accessed directly via it's Project DOI: 10.21228/M8S302 This work is supported by NIH grant, U2C- DK119886.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
| Study ID | ST000466 |
| Study Title | Streptococcus mutans organic acids/amino acid profiles, effect of oxidative stress; pilot |
| Study Type | Amino acid/organic acid profiles of wild-type and mutant strain in response to H2O2 treatment over time. |
| Study Summary | S. mutans UA159 and ΔspxA1 will be grown in BHI to OD600 = 0.4. Each culture will be split in to 4 samples. For the first sample, 3E10 cells will immediately be harvested by fast filtration, scraped off of membrane into ice-cold PBS, and pelleted by centrifugation. The remaining three samples will be treated with H2O2 to 0.5 mM, and the harvesting process repeated after 15, 30 and 60 minutes. |
| Institute | University of Florida |
| Department | SECIM |
| Laboratory | Lemos-Abranches |
| Last Name | Hardin |
| First Name | Emily |
| Address | 1395 Center Drive, PO Box 100424, Gainesville, FL 32610 |
| ehardin@ufl.edu | |
| Phone | 352-273-8844 |
| Submit Date | 2016-09-08 |
| Num Groups | 6 |
| Total Subjects | 6 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | d |
| Analysis Type Detail | LC-MS |
| Release Date | 2017-10-03 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR000358 |
| Project DOI: | doi: 10.21228/M8S302 |
| Project Title: | Streptococcus mutans Amino Acid/Organic Acid Profile |
| Project Summary: | Determination of metabolite profiles of S. mutans strains UA159 (WT) and ΔspxA1 in response to oxidative stress |
| Institute: | University of Florida |
| Department: | Oral Biology |
| Laboratory: | Lemos-Abranches |
| Last Name: | Lemos |
| First Name: | Jose |
| Address: | 1395 Center Drive, PO Box 100424 Gainesville, FL 32610 |
| Email: | jlemos@dental.ufl.edu |
| Phone: | 352-273-8843 |
| Funding Source: | UF start-up funds |
Subject:
| Subject ID: | SU000487 |
| Subject Type: | Bacterial cells |
| Subject Species: | Streptococcus mutans |
| Taxonomy ID: | 1309 |
| Genotype Strain: | UA159 |
| Species Group: | Microorganism |
Factors:
Subject type: Bacterial cells; Subject species: Streptococcus mutans (Factor headings shown in green)
| mb_sample_id | local_sample_id | Strain | Exposure to H2O2 |
|---|---|---|---|
| SA023598 | Lemos_010 | WT | 0.00 |
| SA023599 | Lemos_011 | WT | 15 min |
| SA023600 | Lemos_012 | WT | 30 min |
| SA023601 | Lemos_013 | WT | 60 min |
| SA023602 | Lemos_014 | ΔspxA1 | 0.00 |
| SA023603 | Lemos_017 | ΔspxA1 | 60 min |
| Showing results 1 to 6 of 6 |
Collection:
| Collection ID: | CO000481 |
| Collection Summary: | Upon reaching OD600 = 0.4, the culture is split into 4 samples. Three are treated with H2O2 (0.5 mM). The other is harvested by filtration onto 0.45uM nitrocellulose membrane. The cells will be scraped off of the membrane into ice-cold PBS (~1 mL), centrifuged for 30 seconds at 12K RPM, liquid aspirated and stored at -80C until sending for analysis. This process will be repeated with the remaining three samples after 15, 30 and 60 minutes treatment with H2O2. |
| Sample Type: | Bacterial cells |
Treatment:
| Treatment ID: | TR000501 |
| Treatment Summary: | 0.5 mM H2O2 for 15, 30 and 60 minutes. Control has 0 H2O2 added. |
Sample Preparation:
| Sampleprep ID: | SP000494 |
| Sampleprep Summary: | Amino acids|Organic acids |
| Sampleprep Protocol Filename: | SB_AA_Assay.pdf SB_OA_Assay.pdf |
Combined analysis:
| Analysis ID | AN000728 | AN000729 |
|---|---|---|
| Analysis type | MS | MS |
| Chromatography type | Reversed phase | Reversed phase |
| Chromatography system | Agilent 6490 | Thermo Dionex Ultimate 3000 |
| Column | Waters AccQ Tag (100 x 2mm,1.7um) | Waters Acquity BEH C18 (100 x 2mm,1.7um) |
| MS Type | ESI | ESI |
| MS instrument type | Triple quadrupole | Triple quadrupole |
| MS instrument name | Agilent 6490 QQQ | Thermo Quantiva QQQ |
| Ion Mode | POSITIVE | POSITIVE |
| Units | nmol/mg protein | nmol/mg protein |
Chromatography:
| Chromatography ID: | CH000521 |
| Chromatography Summary: | Amino acids |
| Methods Filename: | SB_AA_Assay.pdf |
| Instrument Name: | Agilent 6490 |
| Column Name: | Waters AccQ Tag (100 x 2mm,1.7um) |
| Column Temperature: | 55 |
| Flow Rate: | 0.7 mL/min |
| Solvent A: | AccQ·Tag Eluent A |
| Solvent B: | accQ·Tag Eluent B |
| Chromatography Type: | Reversed phase |
| Chromatography ID: | CH000522 |
| Chromatography Summary: | Organic acids |
| Methods Filename: | SB_OA_Assay.pdf |
| Instrument Name: | Thermo Dionex Ultimate 3000 |
| Column Name: | Waters Acquity BEH C18 (100 x 2mm,1.7um) |
| Column Temperature: | 45 |
| Flow Rate: | 0.3 mL/min |
| Solvent A: | 100% water; 0.1% formic acid |
| Solvent B: | 100% acetonitrile; 0.1% formic acid |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS000645 |
| Analysis ID: | AN000728 |
| Instrument Name: | Agilent 6490 QQQ |
| Instrument Type: | Triple quadrupole |
| MS Type: | ESI |
| Ion Mode: | POSITIVE |
| MS ID: | MS000646 |
| Analysis ID: | AN000729 |
| Instrument Name: | Thermo Quantiva QQQ |
| Instrument Type: | Triple quadrupole |
| MS Type: | ESI |
| Ion Mode: | POSITIVE |
