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.

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Study IDST002287
Study TitleEnhanced systemic commensal E. coli immunogenicity through minor alteration of the metabolic profile
Study SummaryLC-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
DepartmentMicrobiology and Infectious Disease
LaboratoryGeuking
Last NameBrown
First NameKirsty
AddressHSC 1729, 3330 Hospital Dr NW
Emailkirsty.brown1@ucalgary.ca
Phone2508692232
Submit Date2022-09-26
Raw Data AvailableYes
Raw Data File Type(s)mzXML
Analysis Type DetailLC-MS
Release Date2023-05-04
Release Version1
Kirsty Brown Kirsty Brown
https://dx.doi.org/10.21228/M83H68
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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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

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
SA219142Intra_GP61_1_1Intra GP61 1 1
SA219143Intra_GP61_1_2Intra GP61 1 2
SA219144Intra_GP61_4_1Intra GP61 4 1
SA219145Intra_GP61_4_2Intra GP61 4 2
SA219146Intra_GP61_4_3Intra GP61 4 3
SA219147Intra_GP61_4_4Intra GP61 4 4
SA219148Intra_KO_1_1Intra KO 1 1
SA219149Intra_KO_1_2Intra KO 1 2
SA219150Intra_KO_4_1Intra KO 4 1
SA219151Intra_KO_4_2Intra KO 4 2
SA219152Intra_KO_4_3Intra KO 4 3
SA219153Intra_KO_4_4Intra KO 4 4
SA219154Intra_WT_1_1Intra WT 1 1
SA219155Intra_WT_1_2Intra WT 1 2
SA219156Intra_WT_4_1Intra WT 4 1
SA219157Intra_WT_4_2Intra WT 4 2
SA219158Intra_WT_4_3Intra WT 4 3
SA219159Intra_WT_4_4Intra WT 4 4
SA219160SN_GP61_1_1SN GP61 1 1
SA219161SN_GP61_1_2SN GP61 1 2
SA219162SN_GP61_4_1SN GP61 4 1
SA219163SN_GP61_4_2SN GP61 4 2
SA219164SN_GP61_4_3SN GP61 4 3
SA219165SN_GP61_4_4SN GP61 4 4
SA219166SN_KO_1_1SN KO 1 1
SA219167SN_KO_1_2SN KO 1 2
SA219168SN_KO_4_1SN KO 4 1
SA219169SN_KO_4_2SN KO 4 2
SA219170SN_KO_4_3SN KO 4 3
SA219171SN_KO_4_4SN KO 4 4
SA219172SN_WT_1_1SN WT 1 1
SA219173SN_WT_1_2SN WT 1 2
SA219174SN_WT_4_1SN WT 4 1
SA219175SN_WT_4_2SN WT 4 2
SA219176SN_WT_4_3SN WT 4 3
SA219177SN_WT_4_4SN 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

Combined analysis:

Analysis ID AN003739
Analysis type MS
Chromatography type HILIC
Chromatography system Thermo Vanquish
Column Thermo Syncronis HILIC (100 x 2.1mm,1.7um)
MS Type ESI
MS instrument type Orbitrap
MS instrument name Thermo Q Exactive HF hybrid Orbitrap
Ion Mode NEGATIVE
Units AUC

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

MS:

MS ID:MS003487
Analysis ID:AN003739
Instrument Name:Thermo Q Exactive HF hybrid Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:50-750 m/z, peak integration and assignment using El-Maven software matching to authentic standard library (~150 compounds).
Ion Mode:NEGATIVE
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