Summary of Study ST001421

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 PR000975. The data can be accessed directly via it's Project DOI: 10.21228/M8NX1G This work is supported by NIH grant, U2C- DK119886.

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Study IDST001421
Study TitleMetabolomic study of Escherichia coli K-12 MG1655 WT and its transcriptional regulator mutants under anaerobic fermentation conditions
Study TypeMetabolomics
Study SummaryMetabolomic analysis of Wildtype, fnr, arcA and ihf mutants in glucose minimal media under anaerobic fermentation conditions 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 anaerobically at 37 degrees Celsius and 150 rpm. This study aims to characterize and compare the metabolic profiles of all these strains.
Institute
IIT Bombay
DepartmentDepartment of Chemical Engineering
LaboratorySystems Biology and Metabolic Engineering Laboratory (SBMEL)
Last NamePal
First NameAnkita
AddressDepartment of Chemical Engineering, IIT Bombay, Mumbai, Maharashtra, 400076, India
Emailpal.ankita90@gmail.com
Phone08879536816
Submit Date2020-07-07
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/M8NX1G
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR000975
Project DOI:doi: 10.21228/M8NX1G
Project Title:Metabolomic analysis of Escherichia coli K-12 MG1655 transcriptional regulator mutants under anaerobic conditions
Project Type:Metabolomics
Project Summary:Metabolomic analysis of Wildtype, fnr, arcA and ihf mutants in glucose minimal media under anaerobic fermentation conditions during its exponential phase of growth. Three biological and two technical replicates samples (n=6) were harvested for each of the strains while growing in a bioreactor anaerobically at 37 degrees Celsius and 150 rpm. This study aims to characterize and compare the metabolic profiles 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:Department of Chemical Engineering, IIT Bombay, Mumbai, Maharashtra, 400076, India
Email:pal.ankita90@gmail.com
Phone:08879536816

Subject:

Subject ID:SU001495
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
SA118522ArcA_6Mutant
SA118523ArcA_5Mutant
SA118524ArcA_3Mutant
SA118525IHF_1Mutant
SA118526ArcA_4Mutant
SA118527IHF_3Mutant
SA118528IHF_6Mutant
SA118529IHF_5Mutant
SA118530IHF_4Mutant
SA118531ArcA_2Mutant
SA118532IHF_2Mutant
SA118533ArcA_1Mutant
SA118534FNR_3Mutant
SA118535FNR_1Mutant
SA118536FNR_4Mutant
SA118537FNR_2Mutant
SA118538FNR_5Mutant
SA118539FNR_6Mutant
SA118540WT_3Wildtype
SA118541WT_2Wildtype
SA118542WT_4Wildtype
SA118543WT_6Wildtype
SA118544WT_1Wildtype
SA118545WT_5Wildtype
Showing results 1 to 24 of 24

Collection:

Collection ID:CO001490
Collection Summary:The WT, fnr, arcA and ihf mutants were grown in a bioreactor in glucose minimal media under anaerobic fermentation conditions at 37 degrees Celsius and 150 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_protocol_msi.pdf”.
Collection Protocol Filename:ankita_pal_Extraction_protocol_msi.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:TR001510
Treatment Summary:The WT, fnr, arcA and ihf mutants were grown in a bioreactor in glucose minimal media under anaerobic fermentation conditions at 37 degrees Celsius and 150 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.
Cell Growth Container:Bioreactor
Cell Media:M9 + Glucose
Cell Envir Cond:37 degrees Celsius, 150 rpm. anaerobic fermentation

Sample Preparation:

Sampleprep ID:SP001503
Sampleprep Summary:Samples were extracted from the Wildtype, fnr, arcA and ihf mutants grown in a bioreactor anaerobically in glucose minimal media at 37 degrees Celsius and 150 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.
Sampleprep Protocol Filename:ankita_pal_MS-method_msi.pdf

Combined analysis:

Analysis ID AN002376 AN002377
Analysis type MS MS
Chromatography type HILIC HILIC
Chromatography system Thermo Dionex Ultimate 3000 Thermo Dionex Ultimate 3000
Column SeQuant ZIC-pHILIC (150 x 2.1mm,5um) SeQuant ZIC-pHILIC (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 umol/gDCW and Height ratio/gDCW umol/gDCW

Chromatography:

Chromatography ID:CH001744
Chromatography Summary:The detailed chromatography and MS protocol has been described in "MS-method_msi.pdf" file.
Methods Filename:ankita_pal_MS-method_msi.pdf
Instrument Name:Thermo Dionex Ultimate 3000
Column Name:SeQuant ZIC-pHILIC (150 x 2.1mm,5um)
Flow Rate:200 ul/min
Solvent A:90% acetonitrile/10% water; 10 mM ammonium acetate,pH 9.23
Solvent B:10% acetonitrile/90% water; 10 mM ammonium acetate,pH 9.23
Chromatography Type:HILIC

MS:

MS ID:MS002218
Analysis ID:AN002376
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. Missing value imputation was done using SVD impute function in MetaboAnalyst.
Ion Mode:POSITIVE
  
MS ID:MS002219
Analysis ID:AN002377
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. Missing value imputation was done using SVD impute function in MetaboAnalyst.
Ion Mode:NEGATIVE
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