Summary of Study ST001394

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 PR000957. The data can be accessed directly via it's Project DOI: 10.21228/M80D7P This work is supported by NIH grant, U2C- DK119886.

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Study IDST001394
Study TitleMetabolomic study of Escherichia coli K-12 MG1655 and mutants
Study TypeMetabolomics
Study SummaryMetabolomic analysis of Wildtype, crp mutant and its five adaptively evolved populations evolved in glucose minimal media with 40 mM MOPS during its exponential phase of growth. Three biological and two technical replicate samples (n=6) were harvested for each of the strains while growing in a bioreactor aerobically at 37 degree Celsius and 700 rpm. This study aims to characterize and compare the metabolic profile of all these strains.
Institute
IIT Bombay
DepartmentDepartment of Chemical Engineering
LaboratorySystems Biology and Metabolic Engineering Laboratory
Last NamePal
First NameAnkita
AddressIIT Bombay, Powai, Mumbai - 400076, Maharashtra, India
Emailpal.ankita90@gmail.com
Phone08879536816
Submit Date2020-06-06
Raw Data AvailableYes
Raw Data File Type(s)raw(Thermo)
Analysis Type DetailLC-MS
Release Date2021-03-01
Release Version1
Ankita Pal Ankita Pal
https://dx.doi.org/10.21228/M80D7P
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR000957
Project DOI:doi: 10.21228/M80D7P
Project Title:Metabolomic analysis of Escherichia coli K-12 MG1655
Project Type:Metabolomics
Project Summary:Metabolomic analysis of Wildtype, crp mutant and its five adaptively evolved populations evolved in glucose minimal media with 40 mM MOPS during its exponential phase of growth. Three biological and two technical replicate samples (n=6) were harvested for each of the strains while growing in a bioreactor aerobically at 37 degree Celsius and 700 rpm. This study aims to characterize and compare the metabolic profile of all these strains.
Institute:Indian Institute of Technology Bombay
Department:Department of Chemical Engineering
Laboratory:Systems Biology and Metabolic Engineering Laboratory
Last Name:Pal
First Name:Ankita
Address:IIT Bombay, Powai, Mumbai- 400076, Maharashtra, India
Email:pal.ankita90@gmail.com
Phone:08879536816

Subject:

Subject ID:SU001468
Subject Type:Bacteria
Subject Species:Escherichia coli
Taxonomy ID:562
Genotype Strain:K-12 MG1655

Factors:

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

mb_sample_id local_sample_id Genotype
SA113452Evocrp3_5Evolved
SA113453Evocrp3_6Evolved
SA113454Evocrp4_2Evolved
SA113455Evocrp3_4Evolved
SA113456Evocrp4_1Evolved
SA113457Evocrp3_3Evolved
SA113458Evocrp2_6Evolved
SA113459Evocrp3_1Evolved
SA113460Evocrp3_2Evolved
SA113461Evocrp4_3Evolved
SA113462Evocrp4_4Evolved
SA113463Evocrp5_4Evolved
SA113464Evocrp5_5Evolved
SA113465Evocrp5_6Evolved
SA113466Evocrp5_3Evolved
SA113467Evocrp5_2Evolved
SA113468Evocrp4_5Evolved
SA113469Evocrp4_6Evolved
SA113470Evocrp5_1Evolved
SA113471Evocrp2_5Evolved
SA113472Evocrp2_4Evolved
SA113473Evocrp1_3Evolved
SA113474Evocrp1_2Evolved
SA113475Evocrp1_1Evolved
SA113476Evocrp1_4Evolved
SA113477Evocrp1_5Evolved
SA113478Evocrp2_3Evolved
SA113479Evocrp2_1Evolved
SA113480Evocrp2_2Evolved
SA113481Evocrp1_6Evolved
SA113482Crp_2Parent
SA113483Crp_1Parent
SA113484Crp_3Parent
SA113485Crp_6Parent
SA113486Crp_4Parent
SA113487Crp_5Parent
SA113488WT_3Wildtype
SA113489WT_2Wildtype
SA113490WT_4Wildtype
SA113491WT_6Wildtype
SA113492WT_1Wildtype
SA113493WT_5Wildtype
Showing results 1 to 42 of 42

Collection:

Collection ID:CO001463
Collection Summary:The Wildtype, crp mutant and the five evolved replicate populations were grown in a bioreactor aerobically in glucose minimal media with 40 mM MOPS at 37 degrees Celsius and 700 rpm. The samples were harvested during its exponential phase of growth for three biological and two technical replicates (n=6). The metabolites were extracted using the Methanol-Chloroform-Water method. Detailed sample collection protocol is described in “extraction_method.pdf”.
Sample Type:Bacterial cells
Collection Method:Methanol-Chloroform-Water method
Collection Location:IIT Bombay, Powai, Mumbai- 400076, Mumbai, Maharashtra
Storage Conditions:-80℃

Treatment:

Treatment ID:TR001483
Treatment Summary:The Wildtype, crp mutant and the five evolved replicate populations were grown in a bioreactor aerobically in glucose minimal media with 40 mM MOPS at 37 degrees Celsius and 700 rpm. The metabolites were extracted at expoential phase to characterize and compare the metabolic profiles of all the strains.
Cell Growth Container:Bioreactor
Cell Media:M9 + Glucose + 40 mM MOPS
Cell Envir Cond:37 degrees Celsius, 700 rpm

Sample Preparation:

Sampleprep ID:SP001476
Sampleprep Summary:Samples were extracted from the Wildtype, crp mutant and the five evolved replicate population, grown in a bioreactor aerobically in glucose minimal media with 40 mM MOPS at 37 degrees Celsius and 700 rpm. The metabolites were extracted using the Methanol-Chloroform-Water method. The samples were spiked with an equal volume of 13C-labelled internal standard taken from the same batch at an earlier stage to prevent to account for losses due to metabolite degradation and to enable robust quantification circumventing the ion-suppression effects.

Combined analysis:

Analysis ID AN002332 AN002333
Analysis type MS MS
Chromatography type HILIC HILIC
Chromatography system Thermo Dionex Ultimate 3000 Thermo Dionex Ultimate 3000
Column SeQuant ZIC-HILIC (150 x 2.1mm,5um) SeQuant ZIC-HILIC (150 x 2.1mm,5um)
MS Type ESI ESI
MS instrument type Orbitrap Orbitrap
MS instrument name Thermo Q Exactive Plus Orbitrap Thermo Q Exactive Plus Orbitrap
Ion Mode POSITIVE NEGATIVE
Units Height ratio/gDCW Height ratio/gDCW

Chromatography:

Chromatography ID:CH001709
Chromatography Summary:The detailed chromatography and MS protocol has been described in "ms_method.pdf" file.
Instrument Name:Thermo Dionex Ultimate 3000
Column Name:SeQuant ZIC-HILIC (150 x 2.1mm,5um)
Chromatography Type:HILIC

MS:

MS ID:MS002174
Analysis ID:AN002332
Instrument Name:Thermo Q Exactive Plus Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:Data acquisition done using parent ion MS intensities. Peak height used for processing. Xcalibur 4.3.73.11 used for data analysis and peak integration
Ion Mode:POSITIVE
  
MS ID:MS002175
Analysis ID:AN002333
Instrument Name:Thermo Q Exactive Plus Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:Data acquisition done using parent ion MS intensities. Peak height used for processing. Xcalibur 4.3.73.11 used for data analysis and peak integration
Ion Mode:NEGATIVE
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