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MB Sample ID: SA018746
| Local Sample ID: | SDiamInj04_WT T0_CSH.d |
| Subject ID: | SU000415 |
| Subject Type: | Cells |
| Subject Species: | Synechococcus elongatus PCC 7942 |
| Taxonomy ID: | 1140 |
| Species Group: | Microorganism |
Select appropriate tab below to view additional metadata details:
Subject:
| Subject ID: | SU000415 |
| Subject Type: | Cells |
| Subject Species: | Synechococcus elongatus PCC 7942 |
| Taxonomy ID: | 1140 |
| Species Group: | Microorganism |
Factors:
| Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
|---|---|---|---|---|
| SDiamInj04_WT T0_CSH.d | SA018746 | FL004343 | WT | Genotype |
| SDiamInj04_WT T0_CSH.d | SA018746 | FL004343 | - | Time Point |
Collection:
| Collection ID: | CO000409 |
| Collection Summary: | Bacteria were grown in a turbidostat/bioreactor at equal cell density (measured by optical density at 750nm), under a 12:12h Light/Dark cycle. After collection samples were immediately placed on ice and then centrifuged at 5000RPM for 10min at 4 degrees Celsius. After centrifugation supernatant was decanted and cell pellets were immediately frozen in liquid N2. |
| Collection Protocol Filename: | StudyDesign-SpencerDiamond-10814.pdf |
| Sample Type: | Cell |
| Collection Time: | Samples were collected at T0 (beginning of day) and T4 (4h into day). |
| Volumeoramount Collected: | 40ml of sample was collected at each time point |
| Storage Conditions: | Samples were put into a 50mL conical tube containing ice up to the 30ml mark. |
Treatment:
| Treatment ID: | TR000429 |
| Treatment Summary: | 2: WT bacteria and KaiC mutant The phenotype associated with loss of the core oscillator protein, KaiC, is distinct from that caused by absence of the circadian output transcriptional regulator, RpaA (regulator of phycobilisome-associated A). Untargeted metabolomics analysis and glycogen kinetics suggest that functional KaiC is important for metabolite partitioning in the morning. Additionally, output from the oscillator functions to inhibit RpaA activity in the morning, and kaiC-null strains expressing a mutant KaiC phosphomimetic, KaiC-pST, in which the oscillator is locked in the most active output state, phenocopies a ΔrpaA strain. KaiC-null strains show indications of oxidative pentose phosphate pathway activation as well as increased abundance of primary metabolites. Inhibitory clock output may serve to allow secondary metabolite biosynthesis in the morning, and some metabolites resulting from these processes may feed back to reinforce clock timing. |
| Treatment Protocol Filename: | StudyDesign-SpencerDiamond-10814.pdf |
Sample Preparation:
| Sampleprep ID: | SP000422 |
| Sampleprep Summary: | 1. Add 0.5mL of extraction solvent to tube, gently pipet to remove all cells, transfer cells to 2mL eppendorf tube. Repeat for a total of 1mL extraction solvent + cells in 2mL eppendorf tube. 2. Add 2 small stainless steel grinding beads to eppendorf tube 3. Use the GenoGrinder to grind for 3 minutes at 1,250 rpm. 4. Centrifuge at 14,000xg for 5 minutes. 5. Transfer supernatant to a fresh 2mL eppendorf tube. 6. Add 1mL of extraction solvent to tube containing cell pellet + beads, and repeat steps 3 and 4. 7. Collect supernatant, and combine with supernatant collected in step 5. Total volume of extracted sample will be approximately 2mL. 8. Dry down 50uL of extracted sample in 1.5mL eppendorf tube for GC-TOF analysis. 9. Store backups in -20 or -80C. |
| Sampleprep Protocol Filename: | SOP_Extraction_of_Yeast_Cells.pdf |
Combined analysis:
| Analysis ID | AN000630 | AN000631 |
|---|---|---|
| Analysis type | MS | MS |
| Chromatography type | Reversed phase | Reversed phase |
| Chromatography system | Agilent 6530 | Agilent 6550 |
| Column | Waters Acquity CSH C18 (100 x 2.1mm,1.7um) | Waters Acquity CSH C18 (100 x 2.1mm,1.7um) |
| MS Type | ESI | ESI |
| MS instrument type | QTOF | QTOF |
| MS instrument name | Agilent 6530 QTOF | Agilent 6550 QTOF |
| Ion Mode | POSITIVE | NEGATIVE |
| Units | counts | counts |
Chromatography:
| Chromatography ID: | CH000455 |
| Methods Filename: | Data_Dictionary_Fiehn_laboratory_CSH_QTOF_lipidomics_05-29-2014.pdf |
| Instrument Name: | Agilent 6530 |
| Column Name: | Waters Acquity CSH C18 (100 x 2.1mm,1.7um) |
| Column Pressure: | 450-850 bar |
| Column Temperature: | 65 C |
| Flow Gradient: | 15% B to 99%B |
| Flow Rate: | 0.6 mL/min |
| Internal Standard: | See data dictionary |
| Retention Time: | See data dictionary |
| Sample Injection: | 1.67 uL |
| Solvent A: | 60% acetonitrile/40% water; 10mM formic acid; 10mM ammonium formate |
| Solvent B: | 90% isopropanol/10% acetonitrile; 10mM formic acid; 10mM ammonium formate |
| Analytical Time: | 13 min |
| Capillary Voltage: | 3500 V |
| Time Program: | 15 min |
| Weak Wash Solvent Name: | Isopropanol |
| Strong Wash Solvent Name: | Isopropanol |
| Target Sample Temperature: | Autosampler temp 4 C |
| Randomization Order: | Excel generated |
| Chromatography Type: | Reversed phase |
| Chromatography ID: | CH000456 |
| Methods Filename: | Data_Dictionary_Fiehn_laboratory_CSH_QTOF_lipidomics_05-29-2014.pdf |
| Instrument Name: | Agilent 6550 |
| Column Name: | Waters Acquity CSH C18 (100 x 2.1mm,1.7um) |
| Column Pressure: | 450-850 bar |
| Column Temperature: | 65 C |
| Flow Gradient: | 15% B to 99%B |
| Flow Rate: | 0.6 mL/min |
| Internal Standard: | See data dictionary |
| Retention Time: | See data dictionary |
| Sample Injection: | 5 uL |
| Solvent A: | 40% water/60% acetonitrile; 0.1% formic acid; 10 mM ammonium formate |
| Solvent B: | 90% isopropanol/10% acetonitrile; 10mM acetic acid; 10mM ammonium acetate |
| Analytical Time: | 13 min |
| Capillary Voltage: | 3500 V |
| Time Program: | 15 min |
| Weak Wash Solvent Name: | Isopropanol |
| Strong Wash Solvent Name: | Isopropanol |
| Target Sample Temperature: | Autosampler temp 4 C |
| Randomization Order: | Excel generated |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS000563 |
| Analysis ID: | AN000630 |
| Instrument Name: | Agilent 6530 QTOF |
| Instrument Type: | QTOF |
| MS Type: | ESI |
| Ion Mode: | POSITIVE |
| Capillary Voltage: | 3500 V |
| Collision Gas: | Nitrogen |
| Dry Gas Flow: | 8 L/min |
| Dry Gas Temp: | 325 C |
| Fragment Voltage: | 120 V |
| Fragmentation Method: | Auto MS/MS |
| Ion Source Temperature: | 325 C |
| Ion Spray Voltage: | 1000 V |
| Ionization: | Pos |
| Precursor Type: | Intact Molecule |
| Reagent Gas: | Nitrogen |
| Source Temperature: | 325 C |
| Dataformat: | .d |
| Desolvation Gas Flow: | 11 L/min |
| Desolvation Temperature: | 350 C |
| Nebulizer: | 35 psig |
| Octpole Voltage: | 750 V |
| Resolution Setting: | extended dynamic range |
| Scan Range Moverz: | 60-1700 Da |
| Scanning Cycle: | 2 Hz |
| Scanning Range: | 60-1700 Da |
| Skimmer Voltage: | 65 V |
| MS ID: | MS000564 |
| Analysis ID: | AN000631 |
| Instrument Name: | Agilent 6550 QTOF |
| Instrument Type: | QTOF |
| MS Type: | ESI |
| Ion Mode: | NEGATIVE |
| Capillary Voltage: | 3500 V |
| Collision Gas: | Nitrogen |
| Dry Gas Flow: | 13 L/min |
| Dry Gas Temp: | 200 C |
| Fragment Voltage: | 175 V |
| Fragmentation Method: | Auto MS/MS |
| Ion Source Temperature: | 325 C |
| Ion Spray Voltage: | 1000 V |
| Ionization: | Neg |
| Precursor Type: | Intact Molecule |
| Reagent Gas: | Nitrogen |
| Source Temperature: | 325 C |
| Dataformat: | .d |
| Desolvation Gas Flow: | 11 L/min |
| Desolvation Temperature: | 350 C |
| Nebulizer: | 35 psig |
| Octpole Voltage: | 750 V |
| Resolution Setting: | extended dynamic range |
| Scan Range Moverz: | 60-1700 Da |
| Scanning Cycle: | 2 Hz |
| Scanning Range: | 60-1700 Da |
| Skimmer Voltage: | 65 V |
