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: | Bacteria |
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 |