Summary of study ST000402

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 PR000314. The data can be accessed directly via it's Project DOI: 10.21228/M8V59S This work is supported by NIH grant, U2C- DK119886.

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Study IDST000402
Study TitleImpact of glucose on the central metabolome of C. minutissima
Study SummaryAxenic Chlorella minutissima (UTEX 2341) was grown under mixotrophic and autotrophic conditions to compare metabolome differences. The purpose of this study was to understand how glucose impacted the central metabolome of C. minutissima.
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 Date2016-05-16
Raw Data AvailableYes
Raw Data File Type(s).peg
Analysis Type DetailGC-MS
Release Date2016-06-18
Release Version1
Oliver Fiehn Oliver Fiehn
https://dx.doi.org/10.21228/M8V59S
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR000314
Project DOI:doi: 10.21228/M8V59S
Project Title:Impact of glucose on the central metabolome of C. minutissima
Project Summary:Axenic Chlorella minutissima (UTEX 2341) was grown under mixotrophic and autotrophic conditions to compare metabolome differences. The purpose of this study was to understand how glucose impacted the central metabolome of C. minutissima.
Institute:University of California, Davis
Department:Genome and Biomedical Sciences Facility
Laboratory:WCMC Metabolomics Core
Last Name:Fiehn
First Name:Oliver
Address:1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
Email:ofiehn@ucdavis.edu
Phone:(530) 754-8258
Funding Source:NIH U24DK097154

Subject:

Subject ID:SU000423
Subject Type:Cells
Subject Species:Chlorella minutissima 2341
Taxonomy ID:3081
Species Group:Microorganism

Factors:

Subject type: Cells; Subject species: Chlorella minutissima 2341 (Factor headings shown in green)

mb_sample_id local_sample_id Glucose conc
SA019255140530bmssa12_10 g/L
SA019256140530bmssa11_10 g/L
SA019257140530bmssa10_10 g/L
SA019258140529bmssa45_10 g/L
SA019259140529bmssa47_10 g/L
SA019260140529bmssa22_10 g/L
SA019261140529bmssa23_10 g/L
SA019262140529bmssa30_10 g/L
SA019263140529bmssa46_10 g/L
SA019264140529bmssa33_10 g/L
SA019265140530bmssa08_10 g/L
SA019266140530bmssa07_10 g/L
SA019267140529bmssa44_10 g/L
SA019268140530bmssa09_10 g/L
SA019269140529bmssa36_10 g/L
SA019270140529bmssa21_10 g/L
SA019271140529bmssa34_10 g/L
SA019272140529bmssa35_10 g/L
SA019273140529bmssa31_10 g/L
SA019274140529bmssa20_10 g/L
SA019275140529bmssa08_10 g/L
SA019276140529bmssa09_10 g/L
SA019277140529bmssa10_10 g/L
SA019278140529bmssa07_10 g/L
SA019279140529bmssa06_10 g/L
SA019280140530bmssa24_10 g/L
SA019281140530bmssa23_10 g/L
SA019282140530bmssa22_10 g/L
SA019283140529bmssa11_10 g/L
SA019284140530bmssa21_10 g/L
SA019285140529bmssa49_10 g/L
SA019286140529bmssa48_10 g/L
SA019287140529bmssa19_10 g/L
SA019288140530bmssa19_10 g/L
SA019289140530bmssa20_10 g/L
SA019290140529bmssa18_10 g/L
SA019291140530bmssa02_110 g/L
SA019292140530bmssa04_110 g/L
SA019293140530bmssa15_110 g/L
SA019294140530bmssa16_110 g/L
SA019295140530bmssa17_110 g/L
SA019296140530bmssa18_110 g/L
SA019297140530bmssa01_110 g/L
SA019298140530bmssa14_110 g/L
SA019299140530bmssa06_110 g/L
SA019300140530bmssa13_110 g/L
SA019301140530bmssa05_110 g/L
SA019302140529bmssa37_110 g/L
SA019303140529bmssa14_110 g/L
SA019304140529bmssa15_110 g/L
SA019305140529bmssa16_110 g/L
SA019306140529bmssa17_110 g/L
SA019307140529bmssa13_110 g/L
SA019308140529bmssa12_110 g/L
SA019309140529bmssa02_110 g/L
SA019310140529bmssa03_110 g/L
SA019311140529bmssa04_110 g/L
SA019312140529bmssa05_110 g/L
SA019313140529bmssa24_110 g/L
SA019314140529bmssa25_110 g/L
SA019315140529bmssa40_110 g/L
SA019316140529bmssa41_110 g/L
SA019317140529bmssa42_110 g/L
SA019318140529bmssa43_110 g/L
SA019319140529bmssa39_110 g/L
SA019320140529bmssa01_110 g/L
SA019321140529bmssa26_110 g/L
SA019322140529bmssa27_110 g/L
SA019323140529bmssa28_110 g/L
SA019324140529bmssa29_110 g/L
SA019325140529bmssa50_110 g/L
Showing results 1 to 71 of 71

Collection:

Collection ID:CO000417
Collection Summary:Samples were collected daily from each culture over 5 days (starting at day = 0)
Sample Type:Cells

Treatment:

Treatment ID:TR000437
Treatment Summary:Cultures #1-6 were supplied with 10 g/L glucose, cultures #7-12 were not supplied with glucose (autotrophic)
Treatment Protocol Filename:Objective_2_Exp_6_Mixo_Metabolomics.xlsx
Treatment Protocol Comments:Cultures were grown with 125 ml/min air, 10,000 lux illumination

Sample Preparation:

Sampleprep ID:SP000430
Sampleprep Summary:Quenching 1. Add 5mL of quenching solvent to each 15mL tube, and let sit for at least 30 minutes in ice bath to get to temperature. 2. Add 1mL of cell culture (OD600=1.5) to tube, cap, and gently invert several times. 3. Centrifuge 1,000xg for 5 minutes. 4. Remove supernatant, and store supernatant and cell pellet in -80C until further use. Extraction 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. -20°C bath 5mL quenching solvent 1mL cells+broth
Sampleprep Protocol Filename:SOP_Extraction_of_Yeast_Cells.pdf

Combined analysis:

Analysis ID AN000641
Analysis type MS
Chromatography type GC
Chromatography system Agilent 6890N
Column Restek Corporation Rtx-5Sil MS
MS Type EI
MS instrument type GC Ion Trap
MS instrument name Varian 210-MS GC Ion Trap
Ion Mode POSITIVE
Units counts

Chromatography:

Chromatography ID:CH000466
Methods Filename:Data_Dictionary_Fiehn_laboratory_GCTOF_MS_primary_metabolism_10-15-2013_general.pdf
Instrument Name:Agilent 6890N
Column Name:Restek Corporation Rtx-5Sil MS
Column Pressure:7.7 PSI
Column Temperature:50-330C
Flow Rate:1 ml/min
Injection Temperature:50 C ramped to 250 C by 12 C/s
Sample Injection:0.5 uL
Oven Temperature:50°C for 1 min, then ramped at 20°C/min to 330°C, held constant for 5 min
Transferline Temperature:230C
Washing Buffer:Ethyl Acetate
Sample Loop Size:30 m length x 0.25 mm internal diameter
Randomization Order:Excel generated
Chromatography Type:GC

MS:

MS ID:MS000573
Analysis ID:AN000641
Instrument Name:Varian 210-MS GC Ion Trap
Instrument Type:GC Ion Trap
MS Type:EI
Ion Mode:POSITIVE
Ion Source Temperature:250 C
Ionization Energy:70 eV
Mass Accuracy:Nominal
Source Temperature:250 C
Scan Range Moverz:85-500 Da
Scanning Cycle:17 Hz
Scanning Range:85-500 Da
Skimmer Voltage:1850 V
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