Summary of Study ST001657

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 PR001062. The data can be accessed directly via it's Project DOI: 10.21228/M8F11N This work is supported by NIH grant, U2C- DK119886.

See: https://www.metabolomicsworkbench.org/about/howtocite.php

This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.

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Study IDST001657
Study TitleE.coli K-12 treated by IPL_analysis of organic phase
Study SummaryIn this study, E.coli K-12 was treated by intense pulsed light (IPL) for 0-20 seconds. Then the organic/lipid phase of the cellular metabolome was extracted and submitted to untargeted LC-MS based metabolomic study.
Institute
University of Minnesota
DepartmentFood Science and Nutrition
LaboratoryNutritional Metabolomics
Last NameChen
First NameChi
Address1334 Eckles Ave
Emailchichen@umn.edu
Phone6126247704
Submit Date2021-01-20
Raw Data AvailableYes
Raw Data File Type(s)raw(Waters)
Analysis Type DetailLC-MS
Release Date2021-02-01
Release Version1
Chi Chen Chi Chen
https://dx.doi.org/10.21228/M8F11N
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR001062
Project DOI:doi: 10.21228/M8F11N
Project Title:Effect of IPL on E.coli Metabolome
Project Type:Untargeted LC-MS metabolomic study
Project Summary:Intense pulsed light (IPL) is becoming a new technical platform for disinfecting food against pathogenic bacteria. Metabolic changes are deemed to occur in bacteria as either the causes or the consequences of IPL-elicited bactericidal and bacteriostatic effects. However, little is known about the influences of IPL on bacterial metabolome. In this study, the IPL treatment was ap-plied to E. coli K-12 for 0-20s, leading to time- and dose-dependent changes in E.coli metabolome. We consider the degradation of membrane-bound quinone electron carriers as the trigger of dramatic metabolis shift in IPL-treated E.coli.
Institute:University of Minnesota
Department:Food Science and Nutrition
Laboratory:Nutritional Metabolomics
Last Name:Chen
First Name:Chi
Address:1334 Eckles Ave W, St Paul, MN 55108
Email:chichen@umn.edu
Phone:612-624-7704

Subject:

Subject ID:SU001734
Subject Type:Bacteria
Subject Species:Escherichia coli
Taxonomy ID:562
Genotype Strain:K-12 W3110

Factors:

Subject type: Bacteria; Subject species: Escherichia coli (Factor headings shown in green)

mb_sample_id local_sample_id Treatment
SA151941ctl_2control
SA151942ctl_1control
SA151943ctl_3control
SA151944ctl_4control
SA15192510s_2IPL 10 s
SA15192610s_4IPL 10 s
SA15192710s_1IPL 10 s
SA15192810s_3IPL 10 s
SA15192915s_3IPL 15 s
SA15193015s_4IPL 15 s
SA15193115s_2IPL 15 s
SA15193215s_1IPL 15 s
SA15193320s_1IPL 20 s
SA15193420s_2IPL 20 s
SA15193520s_3IPL 20 s
SA15193620s_4IPL 20 s
SA1519375s_3IPL 5 s
SA1519385s_4IPL 5 s
SA1519395s_1IPL 5 s
SA1519405s_2IPL 5 s
Showing results 1 to 20 of 20

Collection:

Collection ID:CO001727
Collection Summary:E. coli strain K-12 W3110 (ATCC 27325) was cultured on TSA agar medium. A single bacterial colony was picked from TSA agar medium, and then used to inoculate Luria-Bertani broth (EMD Millipore, Billerica, MA). After being incubated at 37 °C for 12 h on a rotary shaker set to 200 rpm, E. coli cells were harvested at an optical density (OD600) of 1, and then centrifuged at 7,500 × g for 10 min in 50 mL centrifuge tubes. After decanting the supernatant, the pellet was washed with phosphate buffered saline (PBS), and then re-suspended to the volume of bacterial culture for further treatment and analysis.
Collection Protocol Filename:Cell_culture_IPL_treatment_Sample_preparation_method.docx
Sample Type:Bacterial cells

Treatment:

Treatment ID:TR001747
Treatment Summary:E.coli K-12 was treated by a customized IPL instrument for 0 - 20 seconds.
Treatment Protocol Filename:Cell_culture_IPL_treatment_Sample_preparation_method.docx

Sample Preparation:

Sampleprep ID:SP001740
Sampleprep Summary:After IPL treatment, the cells were centrifuged and washed with PBS twice. The pellets then went though methanol-water-chloroform extraction for obtaining the organic/non-polar phase.
Sampleprep Protocol Filename:Cell_culture_IPL_treatment_Sample_preparation_method.docx

Combined analysis:

Analysis ID AN002705
Analysis type MS
Chromatography type Reversed phase
Chromatography system Waters Acquity
Column Waters Acquity BEH C8 (100 x 2.1mm,1.7um)
MS Type ESI
MS instrument type QTOF
MS instrument name Waters Xevo-G2-S
Ion Mode POSITIVE
Units no applicable unites

Chromatography:

Chromatography ID:CH001996
Chromatography Summary:analysis of lipids
Instrument Name:Waters Acquity
Column Name:Waters Acquity BEH C8 (100 x 2.1mm,1.7um)
Flow Rate:0.5 mL/min
Solvent A:60% water/40% acetonitrile; 0.1% formic acid; 10 mM ammonium acetate
Solvent B:100% methanol; 0.1% formic acid; 10 mM ammonium acetate
Chromatography Type:Reversed phase

MS:

MS ID:MS002502
Analysis ID:AN002705
Instrument Name:Waters Xevo-G2-S
Instrument Type:QTOF
MS Type:ESI
MS Comments:Ion features were captured by MakerLynx (Waters) after eliminating noises.
Ion Mode:POSITIVE
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