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
| Study ID | ST000173 |
| Study Title | Comparative metabolomics study of WT and iButOH tolerant E. coli |
| Study Summary | This 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 |
| Department | Biomedical Research Core Facilities |
| Laboratory | Metabolomics core |
| Last Name | Kachman |
| First Name | Maureen |
| Address | 6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714 |
| mkachman@umich.edu | |
| Submit Date | 2015-06-04 |
| Num Groups | 4 |
| Total Subjects | 14 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | d |
| Uploaded File Size | 2.0 G |
| Analysis Type Detail | LC-MS |
| Release Date | 2016-06-18 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
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 |
|---|---|---|---|
| SA009446 | S00014364 | iButOH tol mutant | 0.7% (w/v) |
| SA009447 | S00014363 | iButOH tol mutant | 0.7% (w/v) |
| SA009448 | S00014365 | iButOH tol mutant | 0.7% (w/v) |
| SA009443 | S00014371 | iButOH tol mutant | 0% (w/v) |
| SA009444 | S00014369 | iButOH tol mutant | 0% (w/v) |
| SA009445 | S00014370 | iButOH tol mutant | 0% (w/v) |
| SA009438 | S00014358 | WT | 0.7% (w/v) |
| SA009439 | S00014361 | WT | 0.7% (w/v) |
| SA009440 | S00014359 | WT | 0.7% (w/v) |
| SA009441 | S00014360 | WT | 0.7% (w/v) |
| SA009442 | S00014362 | WT | 0.7% (w/v) |
| SA009435 | S00014366 | WT | 0% (w/v) |
| SA009436 | S00014367 | WT | 0% (w/v) |
| SA009437 | S00014368 | WT | 0% (w/v) |
| Showing results 1 to 14 of 14 |
Collection:
| Collection ID: | CO000179 |
| Collection Summary: | - |
| Sample Type: | Cells |
Treatment:
| Treatment ID: | TR000199 |
Sample Preparation:
| Sampleprep ID: | SP000193 |
| Sampleprep Summary: | - |
| 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 |
| Acquisition Parameters File: | QTOF-002-HILIC-35min-1mm-No_Insert.m.zip |
| Processing Parameters File: | EX00268-MassHunterQuant-GlyTCA-LCMS-DataAnalysis-Method.m.zip |
