Summary of Study ST002393

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 PR001540. The data can be accessed directly via it's Project DOI: 10.21228/M8N138 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 IDST002393
Study TitleUntargeted metabolomics analysis of DSS-treated murine intestinal microbiota cultivated in continuous bioreactors
Study SummaryWe cultivated murine faecal microbiota in six replicate continuous bioreactors. Three bioreactors were supplemented with 1% DSS and compared to the untreated control bioreactors.
Institute
Helmholtz Centre for Environmental Research
DepartmentMolecular Systems Biology
Last NameEngelmann
First NameBeatrice
AddressPermoserstrasse 15, 04318 Leipzig, Germany
Emailbeatrice.engelmann@ufz.de
Phone+493411099
Submit Date2022-11-28
Raw Data AvailableYes
Raw Data File Type(s)d
Analysis Type DetailLC-MS
Release Date2022-12-20
Release Version1
Beatrice Engelmann Beatrice Engelmann
https://dx.doi.org/10.21228/M8N138
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR001540
Project DOI:doi: 10.21228/M8N138
Project Title:Untargeted metabolomics analysis of DSS-treated murine intestinal microbiota using continuous cultivation in bioreactors
Project Summary:We cultivated murine faecal microbiota in six replicate continuous bioreactors. Three bioreactors were supplemented with 1% DSS and compared to the untreated control bioreactors.
Institute:Helmholtz Centre for Environmental Research
Department:Molecular Systems Biology
Last Name:Engelmann
First Name:Beatrice
Address:Permoserstrasse 15, 04318 Leipzig, Germany
Email:beatrice.engelmann@ufz.de
Phone:00493411099

Subject:

Subject ID:SU002482
Subject Type:Bacteria
Subject Species:Mus musculus
Taxonomy ID:10090

Factors:

Subject type: Bacteria; Subject species: Mus musculus (Factor headings shown in green)

mb_sample_id local_sample_id Day Treatment
SA238839B_d11_p11 1%DSS
SA238840D_d11_p11 1%DSS
SA238841F_d11_p11 1%DSS
SA238842B_d11_n11 1%DSS
SA238843F_d11_n11 1%DSS
SA238844D_d11_n11 1%DSS
SA238845E_d11_n11 control
SA238846C_d11_n11 control
SA238847A_d11_n11 control
SA238848C_d11_p11 control
SA238849E_d11_p11 control
SA238850A_d11_p11 control
SA238851F_d12_n12 1%DSS
SA238852D_d12_p12 1%DSS
SA238853D_d12_n12 1%DSS
SA238854B_d12_n12 1%DSS
SA238855B_d12_p12 1%DSS
SA238856F_d12_p12 1%DSS
SA238857E_d12_n12 control
SA238858A_d12_p12 control
SA238859A_d12_n12 control
SA238860C_d12_n12 control
SA238861E_d12_p12 control
SA238862C_d12_p12 control
SA238863D_d13_n13 1%DSS
SA238864D_d13_p13 1%DSS
SA238865B_d13_n13 1%DSS
SA238866B_d13_p13 1%DSS
SA238867F_d13_p13 1%DSS
SA238868F_d13_n13 1%DSS
SA238869C_d13_p13 control
SA238870C_d13_n13 control
SA238871A_d13_p13 control
SA238872A_d13_n13 control
SA238873E_d13_p13 control
SA238874E_d13_n13 control
SA238875F_d14_n14 1%DSS
SA238876F_d14_p14 1%DSS
SA238877D_d14_p14 1%DSS
SA238878D_d14_n14 1%DSS
SA238879B_d14_n14 1%DSS
SA238880B_d14_p14 1%DSS
SA238881E_d14_p14 control
SA238882A_d14_n14 control
SA238883C_d14_n14 control
SA238884A_d14_p14 control
SA238885E_d14_n14 control
SA238886C_d14_p14 control
SA238887B_d15_p15 1%DSS
SA238888D_d15_n15 1%DSS
SA238889B_d15_n15 1%DSS
SA238890F_d15_p15 1%DSS
SA238891F_d15_n15 1%DSS
SA238892D_d15_p15 1%DSS
SA238893A_d15_p15 control
SA238894E_d15_p15 control
SA238895E_d15_n15 control
SA238896A_d15_n15 control
SA238897C_d15_n15 control
SA238898C_d15_p15 control
SA238899D_d18_n18 1%DSS
SA238900F_d18_n18 1%DSS
SA238901B_d18_p18 1%DSS
SA238902B_d18_n18 1%DSS
SA238903F_d18_p18 1%DSS
SA238904D_d18_p18 1%DSS
SA238905C_d18_p18 control
SA238906A_d18_p18 control
SA238907C_d18_n18 control
SA238908E_d18_p18 control
SA238909E_d18_n18 control
SA238910A_d18_n18 control
SA238911D_d19_n19 1%DSS
SA238912F_d19_n19 1%DSS
SA238913B_d19_p19 1%DSS
SA238914D_d19_p19 1%DSS
SA238915B_d19_n19 1%DSS
SA238916F_d19_p19 1%DSS
SA238917C_d19_n19 control
SA238918A_d19_p19 control
SA238919C_d19_p19 control
SA238920A_d19_n19 control
SA238921E_d19_n19 control
SA238922E_d19_p19 control
SA238923B_d20_p20 1%DSS
SA238924F_d20_p20 1%DSS
SA238925B_d20_n20 1%DSS
SA238926D_d20_p20 1%DSS
SA238927D_d20_n20 1%DSS
SA238928F_d20_n20 1%DSS
SA238929E_d20_p20 control
SA238930C_d20_p20 control
SA238931A_d20_p20 control
SA238932E_d20_n20 control
SA238933A_d20_n20 control
SA238934C_d20_n20 control
Showing results 1 to 96 of 96

Collection:

Collection ID:CO002475
Collection Summary:Samples were taken at day 1 and as a multiple of 24 h during the control phase (day 12-14) and the early (day 15) and late treatment phase (day 18 to day 20) from the bioreactors under unaerobic conditions.
Sample Type:Feces

Treatment:

Treatment ID:TR002494
Treatment Summary:Faecal pellets were isolated from the colon under aseptic conditions. Directly after collection, faecal pellets were stored at anaerobic conditions. The murine microbiota was cultivated in the chemostats from day 1 to day 13. At day 14, the bioreactors B, D and F were spiked with 1% DSS.

Sample Preparation:

Sampleprep ID:SP002488
Sampleprep Summary:In brief, culture supernatants were thawed and 100 µL were mixed with 500 µL methanol:acetonitrile (ACN):water (2:3:1) followed by vortex and sonication. After centrifugation, 100 µL of the supernatant were dried in a SpeedVac™ vacuum concentrator (Eppendorf, Hamburg, Germany). Prior to measurement, the extract was resuspended in 100 µl 1 % ACN and 0.1 % formic acid in water.

Combined analysis:

Analysis ID AN003898 AN003899
Analysis type MS MS
Chromatography type Reversed phase Reversed phase
Chromatography system Agilent 1260 Agilent 1260
Column Waters Acquity BEH HSS T3 (100 x 2.1mm,1.8um) Waters Acquity BEH HSS T3 (100 x 2.1mm,1.8um)
MS Type ESI ESI
MS instrument type QTOF QTOF
MS instrument name Agilent 6540 QTOF Agilent 6540 QTOF
Ion Mode NEGATIVE POSITIVE
Units Peak area Peak area

Chromatography:

Chromatography ID:CH002886
Instrument Name:Agilent 1260
Column Name:Waters Acquity BEH HSS T3 (100 x 2.1mm,1.8um)
Solvent A:100% water; 0.1% formic acid
Solvent B:100% acetonitrile; 0.1% formic acid
Chromatography Type:Reversed phase

MS:

MS ID:MS003637
Analysis ID:AN003898
Instrument Name:Agilent 6540 QTOF
Instrument Type:QTOF
MS Type:ESI
MS Comments:All samples were acquired in positive and negative ionization mode. The QTOF was set up in centroid mode with a scan range of 60 – 1000 m/z. After each full scan, the five most intense ions (threshold 200 counts) were subjected to fragmentation. The obtained raw data (.d-files) were imported into the Progenesis QI® software (version2.1, Waters Corporation) for further analysis.
Ion Mode:NEGATIVE
  
MS ID:MS003638
Analysis ID:AN003899
Instrument Name:Agilent 6540 QTOF
Instrument Type:QTOF
MS Type:ESI
MS Comments:All samples were acquired in positive and negative ionization mode. The QTOF was set up in centroid mode with a scan range of 60 – 1000 m/z. After each full scan, the five most intense ions (threshold 200 counts) were subjected to fragmentation. The obtained raw data (.d-files) were imported into the Progenesis QI® software (version2.1, Waters Corporation) for further analysis.
Ion Mode:POSITIVE
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