Summary of Study ST002076

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 PR001316. The data can be accessed directly via it's Project DOI: 10.21228/M8M990 This work is supported by NIH grant, U2C- DK119886.

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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.

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Study IDST002076
Study TitleMetabolomic study of Escherichia coli K-12 MG1655 WT and its transcriptional regulator double mutants under anaerobic fermentation conditions
Study TypeMetabolomics
Study SummaryMetabolomic analysis of Wildtype, fnr_arcA (FA), arcA_ihf (AI) and fnr_ihf (FI) 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 Date2022-02-02
Raw Data AvailableYes
Raw Data File Type(s)raw(Thermo)
Analysis Type DetailLC-MS
Release Date2022-06-30
Release Version1
Ankita Pal Ankita Pal
https://dx.doi.org/10.21228/M8M990
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:


Project:

Project ID:PR001316
Project DOI:doi: 10.21228/M8M990
Project Title:Metabolomic analysis of Escherichia coli K-12 MG1655 transcriptional regulator double mutants under anaerobic conditions
Project Type:Metabolomics
Project Summary:Metabolomic analysis of Wildtype, fnr_arcA (FA), arcA_ihf (AI) and fnr_ihf (FI) 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:IIT 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:SU002159
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 KO Type
SA196289AI_3Mutant AI
SA196290AI_4Mutant AI
SA196291AI_6Mutant AI
SA196292AI_2Mutant AI
SA196293AI_5Mutant AI
SA196294AI_1Mutant AI
SA196295FA_6Mutant FA
SA196296FA_2Mutant FA
SA196297FA_5Mutant FA
SA196298FA_1Mutant FA
SA196299FA_4Mutant FA
SA196300FA_3Mutant FA
SA196301FI_1Mutant FI
SA196302FI_2Mutant FI
SA196303FI_4Mutant FI
SA196304FI_5Mutant FI
SA196305FI_3Mutant FI
SA196306FI_6Mutant FI
SA196307WT_2Wildtype Wildtype
SA196308WT_5Wildtype Wildtype
SA196309WT_1Wildtype Wildtype
SA196310WT_6Wildtype Wildtype
SA196311WT_4Wildtype Wildtype
SA196312WT_3Wildtype Wildtype
Showing results 1 to 24 of 24

Collection:

Collection ID:CO002152
Collection Summary:The WT, FA, AI and FI 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: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:TR002171
Treatment Summary:The WT, FA, AI and FI 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:SP002165
Sampleprep Summary:Samples were extracted from the Wildtype, FA, AI and FI 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:Method_msi.pdf

Combined analysis:

Analysis ID AN003383 AN003384
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 and Height ratio/gDCW

Chromatography:

Chromatography ID:CH002501
Chromatography Summary:The detailed chromatography and MS protocol has been described in "Method_msi.pdf" file.
Methods Filename:Method_msi.pdf
Instrument Name:Thermo Dionex Ultimate 3000
Column Name:SeQuant ZIC- pHILIC (150 x 2.1mm, 5um)
Chromatography Type:HILIC

MS:

MS ID:MS003150
Analysis ID:AN003383
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:MS003151
Analysis ID:AN003384
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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