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.
| Study ID | ST001657 |
| Study Title | E.coli K-12 treated by IPL_analysis of organic phase |
| Study Summary | In 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 |
| Department | Food Science and Nutrition |
| Laboratory | Nutritional Metabolomics |
| Last Name | Chen |
| First Name | Chi |
| Address | 1334 Eckles Ave |
| chichen@umn.edu | |
| Phone | 6126247704 |
| Submit Date | 2021-01-20 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | raw(Waters) |
| Analysis Type Detail | LC-MS |
| Release Date | 2021-02-01 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
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 |
|---|---|---|
| SA151941 | ctl_2 | control |
| SA151942 | ctl_1 | control |
| SA151943 | ctl_3 | control |
| SA151944 | ctl_4 | control |
| SA151925 | 10s_2 | IPL 10 s |
| SA151926 | 10s_4 | IPL 10 s |
| SA151927 | 10s_1 | IPL 10 s |
| SA151928 | 10s_3 | IPL 10 s |
| SA151929 | 15s_3 | IPL 15 s |
| SA151930 | 15s_4 | IPL 15 s |
| SA151931 | 15s_2 | IPL 15 s |
| SA151932 | 15s_1 | IPL 15 s |
| SA151933 | 20s_1 | IPL 20 s |
| SA151934 | 20s_2 | IPL 20 s |
| SA151935 | 20s_3 | IPL 20 s |
| SA151936 | 20s_4 | IPL 20 s |
| SA151937 | 5s_3 | IPL 5 s |
| SA151938 | 5s_4 | IPL 5 s |
| SA151939 | 5s_1 | IPL 5 s |
| SA151940 | 5s_2 | IPL 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 |
