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.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
| Study ID | ST001421 |
| Study Title | Metabolomic study of Escherichia coli K-12 MG1655 WT and its transcriptional regulator mutants under anaerobic fermentation conditions |
| Study Type | Metabolomics |
| Study 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 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 |
| Department | Department of Chemical Engineering |
| Laboratory | Systems Biology and Metabolic Engineering Laboratory (SBMEL) |
| Last Name | Pal |
| First Name | Ankita |
| Address | Department of Chemical Engineering, IIT Bombay, Mumbai, Maharashtra, 400076, India |
| pal.ankita90@gmail.com | |
| Phone | 08879536816 |
| Submit Date | 2020-07-07 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | raw(Thermo) |
| Analysis Type Detail | LC-MS |
| Release Date | 2021-03-01 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
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 |
|---|---|---|
| SA118522 | ArcA_6 | Mutant |
| SA118523 | ArcA_5 | Mutant |
| SA118524 | ArcA_3 | Mutant |
| SA118525 | IHF_1 | Mutant |
| SA118526 | ArcA_4 | Mutant |
| SA118527 | IHF_3 | Mutant |
| SA118528 | IHF_6 | Mutant |
| SA118529 | IHF_5 | Mutant |
| SA118530 | IHF_4 | Mutant |
| SA118531 | ArcA_2 | Mutant |
| SA118532 | IHF_2 | Mutant |
| SA118533 | ArcA_1 | Mutant |
| SA118534 | FNR_3 | Mutant |
| SA118535 | FNR_1 | Mutant |
| SA118536 | FNR_4 | Mutant |
| SA118537 | FNR_2 | Mutant |
| SA118538 | FNR_5 | Mutant |
| SA118539 | FNR_6 | Mutant |
| SA118540 | WT_3 | Wildtype |
| SA118541 | WT_2 | Wildtype |
| SA118542 | WT_4 | Wildtype |
| SA118543 | WT_6 | Wildtype |
| SA118544 | WT_1 | Wildtype |
| SA118545 | WT_5 | Wildtype |
| 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 |
