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MB Sample ID: SA094209
| Local Sample ID: | SA7 BR3-2 |
| Subject ID: | SU001372 |
| Subject Type: | Bacteria |
| Subject Species: | Synechococcus elongatus PCC 11801 |
| Taxonomy ID: | 2219813 |
| Genotype Strain: | Synechococcus elongatus PCC 11801 |
Select appropriate tab below to view additional metadata details:
Subject:
| Subject ID: | SU001372 |
| Subject Type: | Bacteria |
| Subject Species: | Synechococcus elongatus PCC 11801 |
| Taxonomy ID: | 2219813 |
| Genotype Strain: | Synechococcus elongatus PCC 11801 |
Factors:
| Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
|---|---|---|---|---|
| SA7 BR3-2 | SA094209 | FL013465 | △DOP62_03525 PpsbaI OgdA PpsbaIII SsaD Pcpcb300 PEPC SmR , DDOP62_03790 Prbcl400 gltA Prbcl400 SBPase/FBPase KanR | Genotype |
Collection:
| Collection ID: | CO001367 |
| Collection Summary: | The experiment was conducted in a shaker maintained at a temperature of 38°C, 1% CO2, and 120 rpm. The cells were grown in 100 ml shake flasks with 20 ml culture volume and the samples for metabolomics analysis were collected at a metabolic steady-state (OD 730 nm = 0.6). Samples were quenched with methanol and extracted using the methanol-chloroform-water method. Extracts were stored at -80°C till LCMS analysis. LCMS analysis was done in the negative ion mode using information-dependent acquisition (IDA) method. |
| Sample Type: | Bacterial cells |
| Collection Tube Temp: | 4 degree centrigrade |
Treatment:
| Treatment ID: | TR001387 |
| Treatment Summary: | The metabolites were extracted using a methanol-chloroform-water method described in the Metabolite Extraction Protocol file of the collection data. |
Sample Preparation:
| Sampleprep ID: | SP001380 |
| Sampleprep Summary: | One aliquot of the metabolite extract of each sample were reconstituted in 100µL 50:50 methanol-water and filtered using nylon syringe filters to remove any particulate matter. The metabolite extract of each test sample was mixed with equal volume of an extract of the PCC 11801 WT biomass that is fully labeled with 13C isotopic carbon by growing for ~5 generations in the presence of NaH13CO3 in modified BG-11 medium. 13C-labeled biomass of PCC 11801 that acted as an internal standard. The injection volume was 6 µL. The peak areas corresponding to the 12C and 13C monoisotopic peak for the metabolites of interest were quantified using MultiQuant 3.0.1 (SCIEX, Framingham, MA). The relative quantification of metabolites was done using isotopic ratio method by normalizing area under the peak for monoisotopic m/z of a particular metabolite by its respective highest possible isotopologue present in the internal standard giving area ratio. |
| Processing Storage Conditions: | On ice |
| Extract Storage: | -80℃ |
Combined analysis:
| Analysis ID | AN002162 |
|---|---|
| Analysis type | MS |
| Chromatography type | Reversed phase |
| Chromatography system | Shimadzu 20AD |
| Column | Phenomenex Synergi Hydro RP 100 A (100 x 2mm,2.5um) |
| MS Type | ESI |
| MS instrument type | QTOF |
| MS instrument name | ABI Sciex 5600+ TripleTOF |
| Ion Mode | NEGATIVE |
| Units | Area Ratio |
Chromatography:
| Chromatography ID: | CH001580 |
| Instrument Name: | Shimadzu 20AD |
| Column Name: | Phenomenex Synergi Hydro RP 100 A (100 x 2mm,2.5um) |
| Flow Gradient: | The gradient method used is as follows: 0% B (0.01 min), 0% B (2 min), 35% B (8 min), 35% B (10.5 min), 90% B (15.50 min), 90% B (20.5 min), 0% B (22 min), and 0% B (30 min) |
| Flow Rate: | 0.3 mL/minute |
| Solvent A: | 100% water; 15 mM acetic acid; 10 mM tributylamine |
| Solvent B: | 100% methanol |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS002011 |
| Analysis ID: | AN002162 |
| Instrument Name: | ABI Sciex 5600+ TripleTOF |
| Instrument Type: | QTOF |
| MS Type: | ESI |
| MS Comments: | The peak areas corresponding to the 12C and 13C monoisotopic peak for the metabolites of interest were quantified using MultiQuant 3.0.1 (SCIEX, Framingham, MA). The relative quantification of metabolites was done using isotopic ratio method by normalizing area under the peak for monoisotopic m/z of a particular metabolite by its respective highest possible isotopologue present in the internal standard giving area ratio. |
| Ion Mode: | NEGATIVE |
