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MB Sample ID: SA094306
| Local Sample ID: | 11801 LDC 31-HR BR1 IS IDA-1 |
| Subject ID: | SU001376 |
| 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: | SU001376 |
| 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 |
|---|---|---|---|---|
| 11801 LDC 31-HR BR1 IS IDA-1 | SA094306 | FL013476 | 31 | Time (h) |
| 11801 LDC 31-HR BR1 IS IDA-1 | SA094306 | FL013476 | MID-DAY | Treatment Condition |
Collection:
| Collection ID: | CO001371 |
| Collection Summary: | Experiments were carried out by growing Synechococcus elongatus PCC 11801 cells in multicultivators designed to provide sinusoidal light. The period was 14:10 (light-dark). The samples for metabolomics analysis were collected in the second diurnal cycle at an interval of 6 hours starting from 25th hour (25, 31, 37 and 43 hours). The light intensity amplitude was 600 µmole photons m-2 s-1. Additionally samples were also collected using cells grown under continuous light illumination of 600 µmole photons m-2 s-1 to compare the difference in metabolite levels compared to that in the diurnal cycle. 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 |
Treatment:
| Treatment ID: | TR001391 |
| Treatment Summary: | The metabolites were extracted using a methanol-chloroform-water method described in the Sample Collection and Treatment Protocol file of the collection data. |
Sample Preparation:
| Sampleprep ID: | SP001384 |
| 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 | AN002168 |
|---|---|
| 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: | CH001586 |
| 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: | MS002017 |
| Analysis ID: | AN002168 |
| 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 |
