Summary of Study ST001664
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 PR001069. The data can be accessed directly via it's Project DOI: 10.21228/M8HQ3X 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 | ST001664 |
| Study Title | E.coli K-12 treated by IPL - analysis of polar phase (part-II) |
| Study Summary | E.coli K-12 cells were treated by IPL, extracted and separated into organic/lipid phase and polar phase. Chemical derivatization with dansyl chloride was applied for analysis of amino acids in the polar phase extraction. |
| Institute | University of Minnesota |
| Last Name | Chen |
| First Name | Chi |
| Address | 1334 Eckles Ave, St Paul, Minnesota, 55108, USA |
| chichen@umn.edu | |
| Phone | 6126247704 |
| Submit Date | 2021-01-25 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | raw(Waters) |
| Analysis Type Detail | LC-MS |
| Release Date | 2021-02-17 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR001069 |
| Project DOI: | doi: 10.21228/M8HQ3X |
| Project Title: | Effect of IPL on E.coli Metabolome hydrophilic phase |
| 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 applied to E. coli K-12 for 0-20s, leading to time- and dose-dependent reductions in colony-forming units (CFU) and morphological changes. Cytoplasmic metabolites of the control and IPL-treated E. coli were examined by the liquid chromatography-mass spectrom-etry (LC-MS)-based metabolomic fingerprinting. The results from multivariate modeling and marker identification indicated that the metabolites in redox response, glycolysis, amino acid and nucleotide metabolism were selectively affected by the IPL treatments. |
| Institute: | University of Minnesota |
| Last Name: | Chen |
| First Name: | Chi |
| Address: | 1334 Eckles Ave, St Paul, Minnesota, 55108, USA |
| Email: | chichen@umn.edu |
| Phone: | 6126247704 |
Subject:
| Subject ID: | SU001741 |
| Subject Type: | Bacteria |
| Subject Species: | Escherichia coli |
| Taxonomy ID: | 562 |
| Subject Comments: | E. coli strain K-12 W3110 |
Factors:
Subject type: Bacteria; Subject species: Escherichia coli (Factor headings shown in green)
| mb_sample_id | local_sample_id | Treatment |
|---|---|---|
| SA152210 | ctl_2 | control |
| SA152211 | ctl_1 | control |
| SA152212 | ctl_3 | control |
| SA152213 | ctl_4 | control |
| SA152194 | 10s_2 | IPL 10 s |
| SA152195 | 10s_4 | IPL 10 s |
| SA152196 | 10s_1 | IPL 10 s |
| SA152197 | 10s_3 | IPL 10 s |
| SA152198 | 15s_3 | IPL 15 s |
| SA152199 | 15s_4 | IPL 15 s |
| SA152200 | 15s_2 | IPL 15 s |
| SA152201 | 15s_1 | IPL 15 s |
| SA152202 | 20s_1 | IPL 20 s |
| SA152203 | 20s_2 | IPL 20 s |
| SA152204 | 20s_3 | IPL 20 s |
| SA152205 | 20s_4 | IPL 20 s |
| SA152206 | 5s_3 | IPL 5 s |
| SA152207 | 5s_4 | IPL 5 s |
| SA152208 | 5s_1 | IPL 5 s |
| SA152209 | 5s_2 | IPL 5 s |
| Showing results 1 to 20 of 20 |
Collection:
| Collection ID: | CO001734 |
| Collection Summary: | E.coli strain K-12 was cultured in LB broth and harvested at OD=1. After centrifuge, cell pellets were harvested and washed with PBS twice. Then the pellet was re-suspended in PBS for further treatment. |
| Collection Protocol Filename: | Cell_culture_IPL_treatment_Sample_preparation_method.docx |
| Sample Type: | Bacterial cells |
Treatment:
| Treatment ID: | TR001754 |
| Treatment Summary: | For each IPL treatment, a 30 mL K-12 suspension in PBS was loaded in a petri dish (15 cm diameter) and then placed under the broad-spectrum light (wavelength 190-1100 nm) in a Z-1000 SteriPulse-XL system (Xenon Corporation, Woburn, MA). The samples were treated with the IPL for 0, 5, 10, 15, and 20 s. |
| Treatment Protocol Filename: | Cell_culture_IPL_treatment_Sample_preparation_method.docx |
Sample Preparation:
| Sampleprep ID: | SP001747 |
| Sampleprep Summary: | The control and IPL-treated E. coli samples were centrifuged for obtaining the pellets, which were then washed with PBS twice. After extraction with methanol-water-chloroform, the polar phase was separated and derivatized with dansyl chloride (DC) for amino acid analysis. |
| Sampleprep Protocol Filename: | Cell_culture_IPL treatment_Sample preparation_method.docx |
Combined analysis:
| Analysis ID | AN002716 |
|---|---|
| Analysis type | MS |
| Chromatography type | Reversed phase |
| Chromatography system | Waters Acquity |
| Column | Waters Acquity BEH C18 (50 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: | CH002004 |
| Instrument Name: | Waters Acquity |
| Column Name: | Waters Acquity BEH C18 (50 x 2.1mm,1.7um) |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS002513 |
| Analysis ID: | AN002716 |
| Instrument Name: | Waters Xevo-G2-S |
| Instrument Type: | QTOF |
| MS Type: | ESI |
| MS Comments: | Features were captured by MarkerLynx (Waters) and processed. The relative intensity of each ion was calculated by normalizing the single ion counts (SIC) versus the total ion counts (TIC) in the whole chromatogram, while setting the TIC arbitrarily to 10,000. |
| Ion Mode: | POSITIVE |
