Summary of Study ST000969

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench,, where it has been assigned Project ID PR000664. The data can be accessed directly via it's Project DOI: 10.21228/M8V68R This work is supported by NIH grant, U2C- DK119886.


This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.

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Study IDST000969
Study TitleImpact of thiamine metabolites and spent medium from Chlorella sorokiniana on metabolism in the green algae Auxenochlorella prototheciodes (part II)
Study SummaryThe purpose of this study is to determine how thiamine metabolites impact central metabolism in Auxenochlorella protothecoides when grown in the presence of glucose. We hypothesize that thiamine metabolites alleviate bottlenecks in the TCA cycle and gluconeogensis, thus allowing for greater starch production when they are present. Cells were grown in bioreactors: 3 control cultures with no thiamine metabolites, 3 cultures received thiamine, 3 recieved HMP, and 3 were grown on residual medium from another algae species - Chlorella sorokiniana. We suspect that this residual medium also contains thiamine metabolites. 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.
University of California, Davis
DepartmentGenome and Biomedical Sciences Facility
LaboratoryWCMC Metabolomics Core
Last NameFiehn
First NameOliver
Address1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
Phone(530) 754-8258
Submit Date2018-05-03
Raw Data AvailableYes
Raw Data File Type(s)cdf
Analysis Type DetailGC-MS
Release Date2018-06-05
Release Version1
Oliver Fiehn Oliver Fiehn application/zip

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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