Summary of Study ST000469
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 PR000360. The data can be accessed directly via it's Project DOI: 10.21228/M8HK59 This work is supported by NIH grant, U2C- DK119886.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
| Study ID | ST000469 |
| Study Title | Enterococcus faecalis nucleotide profiles - pilot |
| Study Type | Comparison between wild-type and mutant strain, as well as providing varying cell count input for WT |
| Study Summary | E. faecalis OG1RF and rel/relQ will be grown in FMC-AUG to OD600 = 0.25. 3E10 cells will be harvested by fast filtration, scraped off of membrane into ice-cold PBS, and pelleted by centrifugation. This process will be repeated with OG1RF only to harvest 3E9 and 3E8 cells. A second OG1RF sample of 3E10 cells will be scraped into formic acid; only acid-soluble extract willl be sent for this sample. |
| Institute | University of Florida |
| Department | SECIM |
| Laboratory | Lemos-Abranches |
| Last Name | Kajfasz |
| First Name | Jessica |
| Address | 1395 Center Drive, PO Box 100424 Gainesville, FL 32610 |
| jkajfasz@dental.ufl.edu | |
| Phone | 352-273-6675 |
| Submit Date | 2016-09-10 |
| Num Groups | 5 |
| Total Subjects | 5 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | raw |
| 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: | PR000360 |
| Project DOI: | doi: 10.21228/M8HK59 |
| Project Title: | Enterococcus faecalis nucleotie profiles |
| Project Summary: | Determination of metabolite profile of E. faecalis OG1RF control as compared to exposure to mupirocin or decoyinine |
| Institute: | University of Florida |
| Department: | Oral Biology |
| Laboratory: | Oral Biology 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: | SU000490 |
| Subject Type: | Bacterial cells |
| Subject Species: | Enterococcus faecalis |
| Taxonomy ID: | 1351 |
| Genotype Strain: | OG1RF |
| Species Group: | Microorganism |
Factors:
Subject type: Bacterial cells; Subject species: Enterococcus faecalis (Factor headings shown in green)
| mb_sample_id | local_sample_id | Strain | Resuspension |
|---|---|---|---|
| SA023663 | rel/relQ_3E10 | (p)ppGpp0 | PBS |
| SA023664 | OG1RF_3E10_acid | WT | 1M Formic Acid |
| SA023665 | OG1RF_3E8 | WT | PBS |
| SA023666 | OG1RF_3E9 | WT | PBS |
| SA023667 | OG1RF_3E10 | WT | PBS |
| Showing results 1 to 5 of 5 |
Collection:
| Collection ID: | CO000484 |
| Collection Summary: | 3E9, 3E10 - upon reaching OD600 = 0.25, 100mL (OG1RF) or 425mL (rel/relQ) will be harvested by filtration onto 0.45uM nitrocellulose membrane. The cells will be scraped off of the membrane into ice-cold PBS or formic acid (~1 mL), centrifuged for 45 seconds at 12K RPM, liquid aspirated and stored at -80C until sending for analysis.|3E8 - (OG1RF only). Upon reaching OD600 = 0.25, 1mL culture will be harvested by 45 seconds centrifugation at 12K RPM, liquid decanted, and stored at -80C until sending for analysis. |
| Sample Type: | Bacterial cells |
Treatment:
| Treatment ID: | TR000504 |
| Treatment Summary: | This pilot study involves no treatment - cells will be grown in chemically defined medium to an OD600 of 0.25 and harvested for analysis |
Sample Preparation:
| Sampleprep ID: | SP000497 |
| Sampleprep Summary: | NAD|NADH |
| Sampleprep Protocol Filename: | SB_NAD-ATP_Assay_Agilent.pdf SB_NADH_Assay_Agilent.pdf |
Combined analysis:
| Analysis ID | AN000732 | AN000733 |
|---|---|---|
| Analysis type | MS | MS |
| Chromatography type | Reversed phase | Reversed phase |
| Chromatography system | Agilent 1290 Infinity | Agilent 1290 Infinity |
| Column | Thermo Hypercarb (50 x 2.1mm,3um) | Waters Acquity HSS T3 (100 x 2.1mm,1.8um) |
| MS Type | ESI | ESI |
| MS instrument type | Triple quadrupole | Triple quadrupole |
| MS instrument name | Agilent 6490 QQQ | Agilent 6490 QQQ |
| Ion Mode | POSITIVE | POSITIVE |
| Units | nmol/mg protein | nmol/mg protein |
Chromatography:
| Chromatography ID: | CH000525 |
| Chromatography Summary: | NAD |
| Methods Filename: | SB_NAD-ATP_Assay_Agilent.pdf |
| Instrument Name: | Agilent 1290 Infinity |
| Column Name: | Thermo Hypercarb (50 x 2.1mm,3um) |
| Chromatography Type: | Reversed phase |
| Chromatography ID: | CH000526 |
| Chromatography Summary: | NADH |
| Methods Filename: | SB_NADH_Assay_Agilent.pdf |
| Instrument Name: | Agilent 1290 Infinity |
| Column Name: | Waters Acquity HSS T3 (100 x 2.1mm,1.8um) |
| Column Temperature: | 30 |
| Flow Rate: | 0.54 mL/min |
| Solvent A: | 100% water; 5 mM ammonium acetate, pH 6 |
| Solvent B: | 100% acetonitrile |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS000649 |
| Analysis ID: | AN000732 |
| Instrument Name: | Agilent 6490 QQQ |
| Instrument Type: | Triple quadrupole |
| MS Type: | ESI |
| MS Comments: | NAD |
| Ion Mode: | POSITIVE |
| MS ID: | MS000650 |
| Analysis ID: | AN000733 |
| Instrument Name: | Agilent 6490 QQQ |
| Instrument Type: | Triple quadrupole |
| MS Type: | ESI |
| MS Comments: | NADH |
| Ion Mode: | POSITIVE |
