Summary of Study ST002971
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 PR001849. The data can be accessed directly via it's Project DOI: 10.21228/M8QB0V 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.
| Study ID | ST002971 |
| Study Title | Untargeted metabolomics of bioluminescent cell at T24h |
| Study Summary | We demonstrated applications of this system using three different engineered Escherichia coli requiring different cofactors (fatty alcohol, bioluminescence light, and alkane biosynthesis). The results showed that the XR/lactose system could enhance the production of each system by ~2-4-fold. Untargeted metabolomics and transcriptomics analyses revealed that XR only enhanced pathways related to specific cofactor utilization. |
| Institute | Vidyasirimedhi Institute of Science and Technology |
| Last Name | Sutthaphirom |
| First Name | Chalermroj |
| Address | 555, Moo 1, Payubnai, Wangchan, Rayong, 21210, Thailand |
| chalermroj.s_s19@vistec.ac.th | |
| Phone | (+66)063-9639915 |
| Submit Date | 2023-11-06 |
| Num Groups | 2 |
| Total Subjects | 10 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | d |
| Analysis Type Detail | LC-MS |
| Release Date | 2023-11-20 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR001849 |
| Project DOI: | doi: 10.21228/M8QB0V |
| Project Title: | A versatile in situ cofactor enhancing system for meeting cellular demands for engineered metabolic pathways |
| Project Summary: | Incorporation of XR/lactose in engineered microbes could enhance the productivity due to enhancing the sugar utilization and cofactors synthesis. Untargeted metabolomics analysis could provide the pathway involving this profound effect in engineered microbes. This study is Part 1/3 of XR/lactose system demonstrated in E. coli for fatty alcohol production |
| Institute: | Vidyasirimedhi Institute of Science and Technology |
| Last Name: | Sutthaphirom |
| First Name: | Chalermroj |
| Address: | 555, Moo 1, Payubnai, Wangchan, Rayong, 21210, Thailand |
| Email: | chalermroj.s_s19@vistec.ac.th |
| Phone: | (+66)063-9639915 |
Subject:
| Subject ID: | SU003084 |
| Subject Type: | Bacteria |
| Subject Species: | Escherichia coli |
| Taxonomy ID: | 562 |
| Genotype Strain: | BL21 (DE3) |
| Cell Biosource Or Supplier: | Novagen |
Factors:
Subject type: Bacteria; Subject species: Escherichia coli (Factor headings shown in green)
| mb_sample_id | local_sample_id | Strain |
|---|---|---|
| SA323064 | T24-cde-2.d.DeMP | lux |
| SA323065 | T24-cde-3.d.DeMP | lux |
| SA323066 | T24-cde-5.d.DeMP | lux |
| SA323067 | T24-cde-6.d.DeMP | lux |
| SA323068 | T24-cde-1.d.DeMP | lux |
| SA323059 | T24-cde-XR-4.d.DeMP | XR |
| SA323060 | T24-cde-XR-5.d.DeMP | XR |
| SA323061 | T24-cde-XR-6.d.DeMP | XR |
| SA323062 | T24-cde-XR-3.d.DeMP | XR |
| SA323063 | T24-cde-XR-2.d.DeMP | XR |
| Showing results 1 to 10 of 10 |
Collection:
| Collection ID: | CO003077 |
| Collection Summary: | Samples (1 mL) were rapidly quenched by adding equal volume of cold 60% methanol/water (-40˚C). The quenched samples were centrifuged for 10 min at 4˚C and 800´g. The supernatant was removed, and the pellets were snap frozen in liquid nitrogen and stored at -80˚C until metabolite extraction. |
| Sample Type: | Bacterial cells |
| Storage Conditions: | -80℃ |
Treatment:
| Treatment ID: | TR003093 |
| Treatment Summary: | Cells were grown in LB media and induced the protein expression with lactose at 25˚C for 24 h. The cells were collected at time 24 h for OD and bioluminescent measurement by spectrophotometer and luminometer. |
| Treatment Compound: | 1 mM lactose |
| Cell Growth Container: | flask |
| Cell Envir Cond: | 25˚C 220 rpm |
Sample Preparation:
| Sampleprep ID: | SP003090 |
| Sampleprep Summary: | The pellets were resuspended in 2 mL of cold 100% methanol (-80˚C) (HPLC grade). The samples were frozen in liquid nitrogen and thawed on ice for 3 cycles for extracting intracellular metabolites. The suspensions were centrifuged at 18,800´g at -9˚C for 30 min. The supernatant was transferred into a new 15 mL falcon tube, frozen in liquid nitrogen, and freeze-dried at -80˚C, 1 mbar, for 16 hours. The dried samples were maintained on ice, resuspended in 500 µL of cold 50% ACN/water (HPLC grade), and centrifuged for 30 min at 18,800´g and at -9˚C. The supernatant was collected and stored at -80˚C until analyzing with mass spectrometry. |
| Processing Storage Conditions: | On ice |
| Extraction Method: | Cold methanol |
| Extract Storage: | -80℃ |
| Sample Resuspension: | 500 µL of 50% ACN/water |
Combined analysis:
| Analysis ID | AN004880 |
|---|---|
| Analysis type | MS |
| Chromatography type | HILIC |
| Chromatography system | Agilent 6560 |
| Column | Agilent Poroshell 120 HILIC-Z (150 x 2.1 mm, 2.7 µm) |
| MS Type | ESI |
| MS instrument type | QTOF |
| MS instrument name | Agilent 6560 Ion Mobility |
| Ion Mode | NEGATIVE |
| Units | abundance |
Chromatography:
| Chromatography ID: | CH003682 |
| Instrument Name: | Agilent 6560 |
| Column Name: | Agilent Poroshell 120 HILIC-Z (150 x 2.1 mm, 2.7 µm) |
| Column Temperature: | 35˚C |
| Flow Gradient: | 0 min: 96%B, 24 min: 65%B |
| Flow Rate: | 0.3 mL/min |
| Solvent A: | 10 mM ammonium acetate pH 9.0 |
| Solvent B: | 10 mM ammonium acetate in 85% acetonitrile/water pH 9.0 |
| Chromatography Type: | HILIC |
MS:
| MS ID: | MS004624 |
| Analysis ID: | AN004880 |
| Instrument Name: | Agilent 6560 Ion Mobility |
| Instrument Type: | QTOF |
| MS Type: | ESI |
| MS Comments: | Raw MS data files (.d) were first demultiplexed using the Agilent De-multiplexing tool (Version 1.0, Agilent Technologies). The demultiplexing data files (.DeMP.d) were recalibrated using IM–MS Reprocessor (Version B.08.00, Agilent Technologies). The reference masses used for mass calibration were m/z 112.985587 and 1033.988109. The CCS calibration was performed by the IM–MS Browser software (Version 10.0, Agilent Technologies). |
| Ion Mode: | NEGATIVE |
