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

Perform statistical analysis  |  Show all samples  |  Show named metabolites  |  Download named metabolite data  
Download mwTab file (text)   |  Download mwTab file(JSON)   |  Download data files (Contains raw data)
Study IDST000469
Study TitleEnterococcus faecalis nucleotide profiles - pilot
Study TypeComparison between wild-type and mutant strain, as well as providing varying cell count input for WT
Study SummaryE. 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
DepartmentSECIM
LaboratoryLemos-Abranches
Last NameKajfasz
First NameJessica
Address1395 Center Drive, PO Box 100424 Gainesville, FL 32610
Emailjkajfasz@dental.ufl.edu
Phone352-273-6675
Submit Date2016-09-10
Num Groups5
Total Subjects5
Raw Data AvailableYes
Raw Data File Type(s)raw
Analysis Type DetailLC-MS
Release Date2017-10-03
Release Version1
Jessica Kajfasz Jessica Kajfasz
https://dx.doi.org/10.21228/M8HK59
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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
SA023663rel/relQ_3E10(p)ppGpp0 PBS
SA023664OG1RF_3E10_acidWT 1M Formic Acid
SA023665OG1RF_3E8WT PBS
SA023666OG1RF_3E9WT PBS
SA023667OG1RF_3E10WT 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)
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
  logo