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MB Sample ID: SA051260
| Local Sample ID: | 150707bctsa03_1 |
| Subject ID: | SU000918 |
| Subject Type: | Cells |
| Subject Species: | Escherichia coli |
| Taxonomy ID: | 562 |
| Species Group: | Microorganism |
Select appropriate tab below to view additional metadata details:
Subject:
| Subject ID: | SU000918 |
| Subject Type: | Cells |
| Subject Species: | Escherichia coli |
| Taxonomy ID: | 562 |
| Species Group: | Microorganism |
Factors:
| Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
|---|---|---|---|---|
| 150707bctsa03_1 | SA051260 | FL009865 | LB OD 2.0 | Treatment |
| 150707bctsa03_1 | SA051260 | FL009865 | Cell Pellets | SampleType |
| 150707bctsa03_1 | SA051260 | FL009865 | E.coli Delta glyA (strain VDC6664) | Strain |
Collection:
| Collection ID: | CO000912 |
| Collection Summary: | Cells were grown overnight in M9 glucose 0.2% (w/v) supplemented with 1 mM glycine at 37 °C, and then were diluted to an OD of 0.03 in M9 glucose 0.2% (w/v) supplemented with 1 mM glycine. Mid-log (OD600=0.5) or late-log (OD600=1) samples were centrifuged for 20 s at 13,500 g and stored at -80 °C. |
| Sample Type: | Cell |
Treatment:
| Treatment ID: | TR000932 |
| Treatment Summary: | Bacteria were grown on Luria Bertani (LB) medium (BD Diagnostics Systems) at 37°C or on M9 minimal medium supplemented with 0.2 % (w/v) glucose and 1 mM glycine |
Sample Preparation:
| Sampleprep ID: | SP000925 |
| Sampleprep Summary: | B6 species [PLP, PNP, pyridoxamine 5'-phosphate (PMP), PL, PN and PM] were extracted from WT and ΔyggS pellets (1.0 ml culture of OD60051.0) in 0.9 ml 5 % (w/v) metaphosphoric acid and 0.1 ml internal standard 4-deoxypyridoxine (73 nmol/ml in 5 % metaphosphoric acid). The suspension was vortexed and sonicated. After centrifugation at 10 000 g for 15 min, the supernatant was filtered and a 50 ml sample was taken for HPLC analysis using fluorescence detection (excitation 328 nm, emission 393 nm). |
Combined analysis:
| Analysis ID | AN001441 |
|---|---|
| Analysis type | MS |
| Chromatography type | GC |
| Chromatography system | Agilent 6890N |
| Column | Restek Rtx-5Sil (30m x 0.25mm,0.25um) |
| MS Type | EI |
| MS instrument type | GC-TOF |
| MS instrument name | Leco Pegasus III GC TOF |
| Ion Mode | POSITIVE |
| Units | Counts |
Chromatography:
| Chromatography ID: | CH001012 |
| Instrument Name: | Agilent 6890N |
| Column Name: | Restek Rtx-5Sil (30m x 0.25mm,0.25um) |
| Column Pressure: | 7.7 PSI (initial condition) |
| Column Temperature: | 50 - 330°C |
| Flow Rate: | 1 ml/min |
| Injection Temperature: | 50°C ramped to 250°C by 12°C/s |
| Sample Injection: | 0.5 uL |
| Oven Temperature: | 50°C for 1 min, then ramped at 20°C/min to 330°C, held constant for 5 min |
| Transferline Temperature: | 230°C |
| Washing Buffer: | Ethyl Acetate |
| Sample Loop Size: | 30 m length x 0.25 mm internal diameter |
| Randomization Order: | Excel generated |
| Chromatography Type: | GC |
MS:
| MS ID: | MS001331 |
| Analysis ID: | AN001441 |
| Instrument Name: | Leco Pegasus III GC TOF |
| Instrument Type: | GC-TOF |
| MS Type: | EI |
| Ion Mode: | POSITIVE |
| Ion Source Temperature: | 250°C |
| Ionization Energy: | 70eV |
| Mass Accuracy: | Nominal |
| Scan Range Moverz: | 85-500 |
| Scanning Cycle: | 17 Hz |
| Scanning Range: | 80-500 Da |
| Skimmer Voltage: | 1850 |
