Return to study ST000969 main page

MB Sample ID: SA057941

Local Sample ID:161115aZKsa24_1
Subject ID:SU001008
Subject Type:Cultured cells
Subject Species:Auxenochlorella protothecoides
Taxonomy ID:3075

Select appropriate tab below to view additional metadata details:


Subject ID:SU001008
Subject Type:Cultured cells
Subject Species:Auxenochlorella protothecoides
Taxonomy ID:3075


Local Sample IDMB Sample IDFactor Level IDLevel ValueFactor Name
161115aZKsa24_1SA057941FL0104042 - HMPTreatment


Collection ID:CO001002
Collection Summary:1 ml algae cell culture was collected, 1 ml 70% MeOH (30% dH2O) at -80 C was added to the algae sample. Tubes were spun at 12,000 rcf to pellet for 2 min at 0 C. Supernatant was decanted and pellets stored at -80 before freeze drying at -45 C. Freeze dried samples were stored at -20 C until submission for extraction.
Collection Protocol Filename:StudyDesignBrendanHiggins7252016.pdf
Sample Type:Cultured cells
Volumeoramount Collected:0.11-3 mg
Storage Conditions:-20℃


Treatment ID:TR001022
Treatment Summary:3 control cultures recieved no thiamine metabolites, 3 cultures received thiamine, 3 recieved HMP, and 3 were grown on residual medium from another algae species - Chlorella sorokiniana. Samples were taken daily from each of these 12 cultures over a 5 day time course so that we can observe build-up of metabolites over time.
Treatment Protocol Filename:StudyDesignBrendanHiggins7252016.pdf

Sample Preparation:

Sampleprep ID:SP001015
Sampleprep Summary:1. Check the pH of methanol (pH 7) 2. Make the extraction solution by mixing methanol, chloroform, and water in proportions of 10 : 3 : 1 3. Rinse the extraction solution for 5 min with nitrogen, making sure that the nitrogen line was flushed out of air before using it for degassing the extraction solvent solution. 4. Add one metal ball to each Eppendorf tube, close, and place in liquid nitrogen. 5. Take the Eppendorf tubes from the liquid nitrogen and place into the tube-holder of the grinder being careful to compensate for weight, maintaining equilibrium. 6. Shake for 30s at a frequency of 25 s-1 and check that the leaves have been ground into a fine powder. Repeat if necessary, submerging in liquid nitrogen first. 7. After grinding add 500μL of pre-chilled extraction solution to each tube one by one to prevent even partial thawing of the sample. Store all samples on ice while finishing this step. 8. Vortex the sample for 20s. 9. Centrifuge for 3min at 14,000 rcf using the centrifuge Eppendorf 5415 D. 10. Remove the whole supernatant into a clean Eppendorf tube. 11. Add 800μL of extraction solvent back into the tube with the pellet and metal ball. 12. Vortex the sample again for 20s. 13. Centrifuge for 3min at 14,000 rcf using the centrifuge Eppendorf 5415 D. 14. Remove the whole supernatant and combine with the previous supernatant. 15. Dry in the Labconco Centrivap cold trap concentrator to complete dryness and submit for derivitization.
Sampleprep Protocol Filename:SOP_Extraction_of_Plant_Samples--Chlamydomonas.pdf

Combined analysis:

Analysis ID AN001583
Analysis type MS
Chromatography type GC
Chromatography system Leco Pegasus III GC
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
Units Counts


Chromatography ID:CH001112
Methods Filename:Data_Dictionary_Fiehn_laboratory_GCTOF_MS_primary_metabolism_10-15-2013_general.pdf
Chromatography Comments:Excel generated
Instrument Name:Leco Pegasus III GC
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:0.5µl
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
Chromatography Type:GC


MS ID:MS001461
Analysis ID:AN001583
Instrument Name:Leco Pegasus III GC TOF
Instrument Type:GC-TOF
MS Type:EI
Ion Source Temperature:250°C
Ionization Energy:70eV
Mass Accuracy:Nominal
Source Temperature:250°C
Scan Range Moverz:85-500
Scanning Cycle:17 Hz
Scanning Range:80-500 Da
Skimmer Voltage:1850 V