Summary of Study ST002287
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 PR001467. The data can be accessed directly via it's Project DOI: 10.21228/M83H68 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 | ST002287 |
| Study Title | Enhanced systemic commensal E. coli immunogenicity through minor alteration of the metabolic profile |
| Study Summary | LC-MS data from the supernatant and cell pellet of cultured commensal E. coli with and without mutations in outer membrane porin C |
| Institute | University of Calgary |
| Department | Microbiology and Infectious Disease |
| Laboratory | Geuking |
| Last Name | Brown |
| First Name | Kirsty |
| Address | HSC 1729, 3330 Hospital Dr NW |
| kirsty.brown1@ucalgary.ca | |
| Phone | 2508692232 |
| Submit Date | 2022-09-26 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzXML |
| Analysis Type Detail | LC-MS |
| Release Date | 2023-05-04 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR001467 |
| Project DOI: | doi: 10.21228/M83H68 |
| Project Title: | Enhanced systemic commensal E. coli immunogenicity through minor alteration of the metabolic profile |
| Project Summary: | LC-MS profiles of supernatant and cell pellet of bacterial culture from commensal E. coli strains with different immunogenicity. |
| Institute: | University of Calgary |
| Department: | Microbiology and Infectious Disease |
| Laboratory: | Geuking |
| Last Name: | Brown |
| First Name: | Kirsty |
| Address: | HSC 1729, 3330 Hospital Dr NW |
| Email: | kirsty.brown1@ucalgary.ca |
| Phone: | 250 869 2232 |
| Funding Source: | Canadian Institute of Health Research |
| Publications: | Enhanced systemic commensal E. coli immunogenicity through minor alteration of the metabolic profile |
| Contributors: | Regula Burkhard1, Mia Koegler1, Kirsty Brown2, Kirsten Wilson1, Lukas Mager2, Amanda Zucoloto2, Carolyn Thomson2, Roopa Hebbandi Nanjundappa1, Braedon McDonald1,3,4, Kathy D. McCoy2,3,4, and Markus B. Geuking1,3,4,* |
Subject:
| Subject ID: | SU002373 |
| Subject Type: | Bacteria |
| Subject Species: | Escherichia coli |
| Taxonomy ID: | 562 |
| Species Group: | Bacteria |
Factors:
Subject type: Bacteria; Subject species: Escherichia coli (Factor headings shown in green)
| mb_sample_id | local_sample_id | sample_site | strain | biologial_rep | technical_rep |
|---|---|---|---|---|---|
| SA219142 | Intra_GP61_1_1 | Intra | GP61 | 1 | 1 |
| SA219143 | Intra_GP61_1_2 | Intra | GP61 | 1 | 2 |
| SA219144 | Intra_GP61_4_1 | Intra | GP61 | 4 | 1 |
| SA219145 | Intra_GP61_4_2 | Intra | GP61 | 4 | 2 |
| SA219146 | Intra_GP61_4_3 | Intra | GP61 | 4 | 3 |
| SA219147 | Intra_GP61_4_4 | Intra | GP61 | 4 | 4 |
| SA219148 | Intra_KO_1_1 | Intra | KO | 1 | 1 |
| SA219149 | Intra_KO_1_2 | Intra | KO | 1 | 2 |
| SA219150 | Intra_KO_4_1 | Intra | KO | 4 | 1 |
| SA219151 | Intra_KO_4_2 | Intra | KO | 4 | 2 |
| SA219152 | Intra_KO_4_3 | Intra | KO | 4 | 3 |
| SA219153 | Intra_KO_4_4 | Intra | KO | 4 | 4 |
| SA219154 | Intra_WT_1_1 | Intra | WT | 1 | 1 |
| SA219155 | Intra_WT_1_2 | Intra | WT | 1 | 2 |
| SA219156 | Intra_WT_4_1 | Intra | WT | 4 | 1 |
| SA219157 | Intra_WT_4_2 | Intra | WT | 4 | 2 |
| SA219158 | Intra_WT_4_3 | Intra | WT | 4 | 3 |
| SA219159 | Intra_WT_4_4 | Intra | WT | 4 | 4 |
| SA219160 | SN_GP61_1_1 | SN | GP61 | 1 | 1 |
| SA219161 | SN_GP61_1_2 | SN | GP61 | 1 | 2 |
| SA219162 | SN_GP61_4_1 | SN | GP61 | 4 | 1 |
| SA219163 | SN_GP61_4_2 | SN | GP61 | 4 | 2 |
| SA219164 | SN_GP61_4_3 | SN | GP61 | 4 | 3 |
| SA219165 | SN_GP61_4_4 | SN | GP61 | 4 | 4 |
| SA219166 | SN_KO_1_1 | SN | KO | 1 | 1 |
| SA219167 | SN_KO_1_2 | SN | KO | 1 | 2 |
| SA219168 | SN_KO_4_1 | SN | KO | 4 | 1 |
| SA219169 | SN_KO_4_2 | SN | KO | 4 | 2 |
| SA219170 | SN_KO_4_3 | SN | KO | 4 | 3 |
| SA219171 | SN_KO_4_4 | SN | KO | 4 | 4 |
| SA219172 | SN_WT_1_1 | SN | WT | 1 | 1 |
| SA219173 | SN_WT_1_2 | SN | WT | 1 | 2 |
| SA219174 | SN_WT_4_1 | SN | WT | 4 | 1 |
| SA219175 | SN_WT_4_2 | SN | WT | 4 | 2 |
| SA219176 | SN_WT_4_3 | SN | WT | 4 | 3 |
| SA219177 | SN_WT_4_4 | SN | WT | 4 | 4 |
| Showing results 1 to 36 of 36 |
Collection:
| Collection ID: | CO002366 |
| Collection Summary: | The different E. coli strains were grown in LB media and subcultured to OD600 = 0.5. |
| Sample Type: | Bacterial cells |
Treatment:
| Treatment ID: | TR002385 |
| Treatment Summary: | E.coli strains were either wild type (MG1655), were deficient in outer membrane porin (OmpC KO) or had a viral epitope from LCMV in place of the OmpC (GP61) |
Sample Preparation:
| Sampleprep ID: | SP002379 |
| Sampleprep Summary: | Metabolites from supernatant were extracted in 100% methanol, precipitated at -20°C for 1 hour, centrifuged and diluted into a linear range (1:20 final dilution) with 50% methanol. To extract intracellular metabolites, bacterial pellet was snap-frozen in liquid nitrogen, resuspended in cell lysis buffer (1M Tris, 5M NaCL, 0.5M EDTA, 10% SDS in H2O) and sonicated. Metabolites were extracted as described above |
Chromatography:
| Chromatography ID: | CH002770 |
| Methods Filename: | protocol.docx |
| Instrument Name: | Thermo Vanquish |
| Column Name: | Thermo Syncronis HILIC (100 x 2.1mm,1.7um) |
| Column Temperature: | 30C |
| Flow Gradient: | 2 stage linear gradient |
| Flow Rate: | 600uL/min |
| Solvent A: | 100% water; 20 mM ammonium formate, pH 3 |
| Solvent B: | 100% acetonitrile; 0.1% formic acid |
| Chromatography Type: | HILIC |
Analysis:
| Analysis ID: | AN003739 |
| Laboratory Name: | Lewis, IA |
| Analysis Type: | MS |
| Acquisition Date: | 2021_02 |
| Software Version: | Xcalibur |
| Operator Name: | Drikic, M |
| Chromatography ID: | CH002770 |
| Num Factors: | 36 |
| Num Metabolites: | 91 |
| Units: | AUC |
