Summary of study ST000173

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 PR000150. The data can be accessed directly via it's Project DOI: 10.21228/M8KG68 This work is supported by NIH grant, U2C- DK119886.

See: https://www.metabolomicsworkbench.org/about/howtocite.php

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Study IDST000173
Study TitleComparative metabolomics study of WT and iButOH tolerant E. coli
Study SummaryThis study aims to elucidate metabolic mechanisms of tolerance to isobutanol in E. coli. Two strains are utilized: WT parental strain EcHW24, and isobutanol tolerant strain 38-20-4 created via multiplex genome engineering. The metabolic response to growth with isobutanol (0.7% w/v) and without (0% w/v) on NG50 minimal media will be compared for each strain. 3 replicates for each strain/iButOH concentration have been submitted, excpet for WT/0.7%; we have observed high growth phenotype variation for this combination, and have corresponding submitted 5x replicates. Strain 38-20-4 contains mutations in the TCA cycle (gltA SNP) and amino acid metabolism (loss-of-function indels in glnE, gltD, and tnaA), thus our hypothesis is that tolerance arises via rewiring of TCA cycle and amino acid metabolism, possibly resulting in increased intracellular ratio of glutamine:glutamate
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
Email mkachman@umich.edu
Submit Date2015-06-04
Num Groups4
Total Subjects14
Raw Data AvailableYes
Raw Data File Type(s).xml,.xsd,.stg, .bin, .cd,.cG, .m
Uploaded File Size2.0 G
Analysis Type DetailLC-MS
Release Date2016-06-18
Release Version1
Maureen Kachman Maureen Kachman
https://dx.doi.org/10.21228/M8KG68
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR000150
Project DOI:doi: 10.21228/M8KG68
Project Title:Evolutionary-genomics approach for elucidating and improving complex phenotypes
Project Summary:Genome evolution and engineering to study isobutanol tolerance in E. coli
Institute:University of Michigan
Department:Chemical Engineering
Laboratory:Lin Lab
Last Name:Lin
First Name:Nina
Address:Ann Arbor, MI
Email:ninalin@umich.edu
Phone:734-647-8026

Subject:

Subject ID:SU000192
Subject Type:Bacterial cells
Subject Species:Escherichia coli
Taxonomy ID:562
Species Group:Microorganism

Factors:

Subject type: Bacterial cells; Subject species: Escherichia coli (Factor headings shown in green)

mb_sample_id local_sample_id Strain iButOH concentration
SA009446S00014364iButOH tol mutant 0.7% (w/v)
SA009447S00014363iButOH tol mutant 0.7% (w/v)
SA009448S00014365iButOH tol mutant 0.7% (w/v)
SA009443S00014371iButOH tol mutant 0% (w/v)
SA009444S00014369iButOH tol mutant 0% (w/v)
SA009445S00014370iButOH tol mutant 0% (w/v)
SA009438S00014358WT 0.7% (w/v)
SA009439S00014361WT 0.7% (w/v)
SA009440S00014359WT 0.7% (w/v)
SA009441S00014360WT 0.7% (w/v)
SA009442S00014362WT 0.7% (w/v)
SA009435S00014366WT 0% (w/v)
SA009436S00014367WT 0% (w/v)
SA009437S00014368WT 0% (w/v)
Showing results 1 to 14 of 14

Collection:

Collection ID:CO000179
Sample Type:Cells

Treatment:

Treatment ID:TR000199

Sample Preparation:

Sampleprep ID:SP000193
Sampleprep Protocol Filename:Gly-TCA-nucleotides_analysis_protocol-2015-03-09.docx

Combined analysis:

Analysis ID AN000267
Analysis type MS
Chromatography type HILIC
Chromatography system Agilent 1260
Column Phenomenex Luna NH2 (150 x 1mm, 3um)
MS Type ESI
MS instrument type QTOF
MS instrument name Agilent 6520 QTOF
Ion Mode NEGATIVE
Units pmol/µg protein

Chromatography:

Chromatography ID:CH000190
Methods ID:AQM020
Methods Filename:QTOF-002-HILIC-35min-1mm-No_Insert.m.zip
Instrument Name:Agilent 1260
Column Name:Phenomenex Luna NH2 (150 x 1mm, 3um)
Chromatography Type:HILIC

MS:

MS ID:MS000216
Analysis ID:AN000267
Instrument Name:Agilent 6520 QTOF
Instrument Type:QTOF
MS Type:ESI
Ion Mode:NEGATIVE
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