Summary of Study ST000692

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 PR000414. The data can be accessed directly via it's Project DOI: 10.21228/M8J88N This work is supported by NIH grant, U2C- DK119886.

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Study IDST000692
Study TitleMetabolites produced by strains associated with inflammation
Study TypeMS analysis
Study SummaryEXPERIMENT 1: identify commonalities and differences between species at late log phase. EXPERIMENT 2: identify commonalities and differences within a species in function of the media used for the subset of bacteria cultured in more than one media. EXPERIMENT 3: identify commonalities and differences within a species in function of the growth phase for the subset of strains for which more than one time point was taken during the growth phase. Factor 1: growth phase for this slow growers as defined by early, mid and late log phase. Factor 2:rich media used for growth which are either NOS or OMIZ supplemented or not of TPP (thiamine pyrophosphate) a required supplement for some strains. Factor 3: cell pellet and supernatant of culture in which bacetria excrete small molecules. Factor 4. the bacterial species. All those bacteria come from the same genus and have been isolated in function of inflmmatory conditions in human.
Institute
University of Michigan
DepartmentBiomedical Research Core Facilities
LaboratoryMetabolomics core
Last NameKachman
First NameMaureen
Address6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Emailmkachman@med.umich.edu
Phone(734) 232-8175
Submit Date2017-06-19
Num Groups27
Total Subjects5
Raw Data AvailableYes
Raw Data File Type(s)d
Analysis Type DetailLC-MS
Release Date2017-12-06
Release Version1
Maureen Kachman Maureen Kachman
https://dx.doi.org/10.21228/M8J88N
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR000414
Project DOI:doi: 10.21228/M8J88N
Project Title:Stool and microbial metabolomics
Project Summary:Digestive tract metabolomics in the context of diet
Institute:The Forsyth Institute
Last Name:Izard
First Name:Jacques
Address:Cambridge, MA
Email:jizard@forsyth.org
Phone:617-892-8279

Subject:

Subject ID:SU000715
Subject Type:Bacteria
Subject Species:Treponema pectinovorum
Taxonomy ID:164
Species Group:Bacteria

Factors:

Subject type: Bacteria; Subject species: Treponema pectinovorum (Factor headings shown in green)

mb_sample_id local_sample_id Fraction Growth media Growth phase Sample type species
SA039200S00014845Cells NOS with TPP Early log phase Cells, Cultured denticola
SA039201S00014835Cells NOS with TPP Early log phase Cells, Cultured denticola
SA039202S00014839Cells NOS with TPP Late log phase Cells, Cultured denticola
SA039203S00014849Cells NOS with TPP Late log phase Cells, Cultured denticola
SA039204S00014831Cells NOS with TPP Late log phase Cells, Cultured medium
SA039205S00014825Cells NOS with TPP Late log phase Cells, Cultured phagedenis
SA039206S00014827Cells NOS with TPP Late log phase Cells, Cultured vincentii
SA039207S00014837Cells NOS with TPP Mid log phase Cells, Cultured denticola
SA039208S00014847Cells NOS with TPP Mid log phase Cells, Cultured denticola
SA039214S00014821Cells OMIZ Late log phase Cells, Cultured maltophilum
SA039215S00014823Cells OMIZ Late log phase Cells, Cultured parvum
SA039216S00014819Cells OMIZ Late log phase Cells, Cultured pectinovorum
SA039217S00014829Cells OMIZ Late log phase Cells, Cultured vincentii
SA039209S00014853Cells OMIZ with TPP Late log phase Cells, Cultured denticola
SA039210S00014843Cells OMIZ with TPP Late log phase Cells, Cultured denticola
SA039211S00014833Cells OMIZ with TPP Late log phase Cells, Cultured medium
SA039212S00014851Cells OMIZ with TPP Mid log phase Cells, Cultured denticola
SA039213S00014841Cells OMIZ with TPP Mid log phase Cells, Cultured denticola
SA039218S00014855Control media NOS + TPP control media Culture none
SA039220S00014856Control media OMIZ control media Culture none
SA039219S00014857Control media OMIZ + TPP control media Culture none
SA039221S00016520Culture - - - -
SA039222S00016521Culture - - - -
SA039223S00020136Pooled cells Pooled cells Pooled cells Pooled sample Pooled cells
SA039225S00020134Pooled culture Pooled culture Pooled culture Pooled sample Pooled culture
SA039224S00020135Pooled culture media Pooled culture media Pooled culture media Pooled sample Pooled culture media
SA039226S00014836Supernatant NOS with TPP Early log phase Culture Media denticola
SA039227S00014846Supernatant NOS with TPP Early log phase Culture Media denticola
SA039228S00014850Supernatant NOS with TPP Late log phase Culture Media denticola
SA039229S00014840Supernatant NOS with TPP Late log phase Culture Media denticola
SA039230S00014832Supernatant NOS with TPP Late log phase Culture Media medium
SA039231S00014826Supernatant NOS with TPP Late log phase Culture Media phagedenis
SA039232S00014828Supernatant NOS with TPP Late log phase Culture Media vincentii
SA039233S00014848Supernatant NOS with TPP Mid log phase Culture Media denticola
SA039234S00014838Supernatant NOS with TPP Mid log phase Culture Media denticola
SA039240S00014822Supernatant OMIZ Late log phase Culture Media maltophilum
SA039241S00014824Supernatant OMIZ Late log phase Culture Media parvum
SA039242S00014820Supernatant OMIZ Late log phase Culture Media pectinovorum
SA039243S00014830Supernatant OMIZ Late log phase Culture Media vincentii
SA039235S00014854Supernatant OMIZ with TPP Late log phase Culture Media denticola
SA039236S00014844Supernatant OMIZ with TPP Late log phase Culture Media denticola
SA039237S00014834Supernatant OMIZ with TPP Late log phase Culture Media medium
SA039238S00014842Supernatant OMIZ with TPP Mid log phase Culture Media denticola
SA039239S00014852Supernatant OMIZ with TPP Mid log phase Culture Media denticola
Showing results 1 to 44 of 44

Collection:

Collection ID:CO000709
Collection Summary:-
Sample Type:Bacterial cells

Treatment:

Treatment ID:TR000729
Treatment Summary:-

Sample Preparation:

Sampleprep ID:SP000722
Sampleprep Summary:-
Sampleprep Protocol Filename:A003_-_Untargeted_Metabolomics.pdf

Combined analysis:

Analysis ID AN001069 AN001070
Analysis type MS MS
Chromatography type Reversed phase Reversed phase
Chromatography system Agilent Agilent
Column Waters Acquity HSS T3 (50 x 2.1mm,1.8um) Waters Acquity HSS T3 (50 x 2.1mm,1.8um)
MS Type ESI ESI
MS instrument type QTOF QTOF
MS instrument name Agilent 6530 QTOF Agilent 6530 QTOF
Ion Mode NEGATIVE POSITIVE
Units peak area peak area

Chromatography:

Chromatography ID:CH000755
Instrument Name:Agilent
Column Name:Waters Acquity HSS T3 (50 x 2.1mm,1.8um)
Chromatography Type:Reversed phase

MS:

MS ID:MS000964
Analysis ID:AN001069
Instrument Name:Agilent 6530 QTOF
Instrument Type:QTOF
MS Type:ESI
Ion Mode:NEGATIVE
Analysis Protocol File:A003_-_Untargeted_Metabolomics.pdf
  
MS ID:MS000965
Analysis ID:AN001070
Instrument Name:Agilent 6530 QTOF
Instrument Type:QTOF
MS Type:ESI
Ion Mode:POSITIVE
Analysis Protocol File:A003_-_Untargeted_Metabolomics.pdf
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