Summary of study ST000968

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, 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.

See: https://www.metabolomicsworkbench.org/about/howtocite.php

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 IDST000968
Study TitleImpact of thiamine metabolites and spent medium from Chlorella sorokiniana on metabolism in the green algae Auxenochlorella prototheciodes (part I)
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.
Institute
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
Emailofiehn@ucdavis.edu
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
https://dx.doi.org/10.21228/M8V68R
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:


Project:

Project ID:PR000664
Project DOI:doi: 10.21228/M8V68R
Project Title:Impact of thiamine metabolites and spent medium from Chlorella sorokiniana on metabolism in the green algae Auxenochlorella prototheciodes
Project Summary:The 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.
Institute:Auburn University
Department:College of Engineering
Laboratory:Bioprocess Engineering
Last Name:Higgins
First Name:Brendan
Address:203 Corley Building Auburn, Alabama 36849
Email:bth0023@auburn.edu
Phone:(334) 844-3532

Subject:

Subject ID:SU001007
Subject Type:Cultured cells
Subject Species:Auxenochlorella protothecoides
Taxonomy ID:3075

Factors:

Subject type: Cultured cells; Subject species: Auxenochlorella protothecoides (Factor headings shown in green)

mb_sample_id local_sample_id Treatment
SA057848161109aOEsa16_11 - Control
SA057849161108aOEsa21_11 - Control
SA057850161108aOEsa37_11 - Control
SA057851161108aOEsa27_11 - Control
SA057852161108aOEsa40_11 - Control
SA057853161108aOEsa16_11 - Control
SA057854161108aOEsa33_11 - Control
SA057855161108aOEsa11_11 - Control
SA057856161108aOEsa09_11 - Control
SA057857161109aOEsa01_11 - Control
SA057858161109aOEsa06_11 - Control
SA057859161109aOEsa08_11 - Control
SA057860161108aOEsa45_11 - Control
SA057861161108aOEsa03_11 - Control
SA057862161108aOEsa46_11 - Control
SA057863161108aOEsa48_11 - Control
SA057864161109aOEsa11_11 - Control
SA057865161108aOEsa31_11 - Control
SA057866161108aOEsa42_12 - Thiamine
SA057867161108aOEsa30_22 - Thiamine
SA057868161109aOEsa05_12 - Thiamine
SA057869161108aOEsa23_12 - Thiamine
SA057870161109aOEsa14_12 - Thiamine
SA057871161108aOEsa29_22 - Thiamine
SA057872161108aOEsa13_12 - Thiamine
SA057873161108aOEsa35_12 - Thiamine
SA057874161108aOEsa25_12 - Thiamine
SA057875161108aOEsa14_12 - Thiamine
SA057876161108aOEsa28_22 - Thiamine
SA057877161109aOEsa03_12 - Thiamine
SA057878161108aOEsa08_12 - Thiamine
SA057879161108aOEsa22_12 - Thiamine
SA057880161108aOEsa24_12 - Thiamine
SA057881161109aOEsa21_12 - Thiamine
SA057882161109aOEsa04_12 - Thiamine
SA057883161108aOEsa02_12 - Thiamine
SA057884161109aOEsa22_13 - HMP
SA057885161109aOEsa09_13 - HMP
SA057886161108aOEsa18_13 - HMP
SA057887161108aOEsa04_13 - HMP
SA057888161109aOEsa07_13 - HMP
SA057889161108aOEsa17_13 - HMP
SA057890161109aOEsa15_13 - HMP
SA057891161108aOEsa44_13 - HMP
SA057892161108aOEsa12_13 - HMP
SA057893161108aOEsa47_13 - HMP
SA057894161109aOEsa18_13 - HMP
SA057895161108aOEsa19_13 - HMP
SA057896161108aOEsa10_13 - HMP
SA057897161109aOEsa19_13 - HMP
SA057898161108aOEsa34_13 - HMP
SA057899161108aOEsa06_13 - HMP
SA057900161109aOEsa13_13 - HMP
SA057901161108aOEsa15_13 - HMP
SA057902161108aOEsa36_14 - Residual
SA057903161108aOEsa38_14 - Residual
SA057904161108aOEsa05_14 - Residual
SA057905161108aOEsa07_14 - Residual
SA057906161108aOEsa20_14 - Residual
SA057907161108aOEsa50_14 - Residual
SA057908161109aOEsa02_14 - Residual
SA057909161109aOEsa12_14 - Residual
SA057910161108aOEsa39_14 - Residual
SA057911161108aOEsa41_14 - Residual
SA057912161109aOEsa17_14 - Residual
SA057913161108aOEsa43_14 - Residual
SA057914161108aOEsa32_14 - Residual
SA057915161108aOEsa49_14 - Residual
SA057916161108aOEsa01_14 - Residual
SA057917161109aOEsa20_14 - Residual
SA057918161109aOEsa10_14 - Residual
SA057919161108aOEsa26_14 - Residual
Showing results 1 to 72 of 72

Collection:

Collection ID:CO001001
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:StudyDesignBrendanHiggins782016.pdf
Sample Type:Cultured cells
Volumeoramount Collected:0.15-1 mg
Storage Conditions:-20℃

Treatment:

Treatment ID:TR001021
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:StudyDesignBrendanHiggins782016.pdf

Sample Preparation:

Sampleprep ID:SP001014
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 AN001582
Analysis type MS
Chromatography type GC
Chromatography system Leco Pegasus III GC
Column Restek Rtx-5Sil MS (30 x 0.25mm, 0.25um)
MS Type EI
MS instrument type GC-TOF
MS instrument name Leco Pegasus III GC TOF
Ion Mode POSITIVE
Units Counts

Chromatography:

Chromatography ID:CH001111
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 MS (30 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:

MS ID:MS001460
Analysis ID:AN001582
Instrument Name:Leco Pegasus III GC TOF
Instrument Type:GC-TOF
MS Type:EI
Ion Mode:POSITIVE
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
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