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MB Sample ID: SA118539
| Local Sample ID: | FNR_6 |
| Subject ID: | SU001495 |
| Subject Type: | Bacteria |
| Subject Species: | Escherichia coli |
| Taxonomy ID: | 562 |
| Genotype Strain: | K-12 MG1655 |
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Subject:
| Subject ID: | SU001495 |
| Subject Type: | Bacteria |
| Subject Species: | Escherichia coli |
| Taxonomy ID: | 562 |
| Genotype Strain: | K-12 MG1655 |
Factors:
| Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
|---|---|---|---|---|
| FNR_6 | SA118539 | FL014839 | Mutant | Genotype |
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 |
