Summary of study ST000969

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 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.
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:SU001008
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
SA057920161115aZKsa47_11 - Control
SA057921161115aZKsa43_11 - Control
SA057922161116aZKsa08_21 - Control
SA057923161116aZKsa22_21 - Control
SA057924161115aZKsa10_11 - Control
SA057925161115aZKsa04_11 - Control
SA057926161116aZKsa06_21 - Control
SA057927161116aZKsa14_21 - Control
SA057928161115aZKsa07_11 - Control
SA057929161115aZKsa49_11 - Control
SA057930161115aZKsa39_11 - Control
SA057931161115aZKsa17_11 - Control
SA057932161116aZKsa17_11 - Control
SA057933161115aZKsa28_11 - Control
SA057934161115aZKsa08_11 - Control
SA057935161116aZKsa03_21 - Control
SA057936161115aZKsa13_11 - Control
SA057937161115aZKsa31_11 - Control
SA057938161115aZKsa25_12 - HMP
SA057939161116aZKsa05_22 - HMP
SA057940161115aZKsa22_12 - HMP
SA057941161115aZKsa24_12 - HMP
SA057942161116aZKsa16_12 - HMP
SA057943161115aZKsa40_12 - HMP
SA057944161116aZKsa09_22 - HMP
SA057945161115aZKsa29_12 - HMP
SA057946161115aZKsa12_12 - HMP
SA057947161115aZKsa03_12 - HMP
SA057948161116aZKsa02_22 - HMP
SA057949161116aZKsa12_32 - HMP
SA057950161115aZKsa05_12 - HMP
SA057951161115aZKsa15_12 - HMP
SA057952161116aZKsa10_22 - HMP
SA057953161115aZKsa50_12 - HMP
SA057954161115aZKsa27_12 - HMP
SA057955161115aZKsa01_12 - HMP
SA057956161116aZKsa21_13 - Residual
SA057957161116aZKsa04_23 - Residual
SA057958161115aZKsa45_13 - Residual
SA057959161115aZKsa19_13 - Residual
SA057960161115aZKsa32_13 - Residual
SA057961161115aZKsa02_13 - Residual
SA057962161115aZKsa23_13 - Residual
SA057963161115aZKsa41_13 - Residual
SA057964161116aZKsa01_23 - Residual
SA057965161115aZKsa30_13 - Residual
SA057966161116aZKsa07_23 - Residual
SA057967161116aZKsa11_33 - Residual
SA057968161116aZKsa20_13 - Residual
SA057969161115aZKsa36_13 - Residual
SA057970161115aZKsa37_13 - Residual
SA057971161115aZKsa26_13 - Residual
SA057972161115aZKsa11_13 - Residual
SA057973161115aZKsa46_13 - Residual
SA057974161116aZKsa18_14 - Thiamine
SA057975161115aZKsa38_14 - Thiamine
SA057976161115aZKsa09_14 - Thiamine
SA057977161115aZKsa48_14 - Thiamine
SA057978161115aZKsa20_14 - Thiamine
SA057979161115aZKsa34_14 - Thiamine
SA057980161115aZKsa35_14 - Thiamine
SA057981161116aZKsa13_14 - Thiamine
SA057982161115aZKsa33_14 - Thiamine
SA057983161115aZKsa42_14 - Thiamine
SA057984161115aZKsa18_14 - Thiamine
SA057985161115aZKsa44_14 - Thiamine
SA057986161115aZKsa14_14 - Thiamine
SA057987161115aZKsa16_14 - Thiamine
SA057988161115aZKsa21_14 - Thiamine
SA057989161115aZKsa06_14 - Thiamine
SA057990161116aZKsa15_24 - Thiamine
SA057991161116aZKsa19_14 - Thiamine
Showing results 1 to 72 of 72

Collection:

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:

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 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: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 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:MS001461
Analysis ID:AN001583
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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