Summary of Study ST000117

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 PR000106. The data can be accessed directly via it's Project DOI: 10.21228/M8RC75 This work is supported by NIH grant, U2C- DK119886.


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Study IDST000117
Study TitleMetabolomics analysis of multiple metabolic functions in the YjgF/YER057c/UK114 (Rid) protein family GC-MS (Part 1)
Study Typewildtype vs knock-out
Study SummaryMetabolomics analysis of wild-type S. enterica, single RidA knock-out and triple Rid (ridA Rid2 Rid7) knock-out S.enterica cells
University of California, Davis
DepartmentGenome Center
LaboratoryFiehn Laboratory
Last NameElBadawi-Sidhu
First NameMona
Address451 Health Sciences Drive, Davis, California 95616, USA
Submit Date2014-11-06
Num Groups3
Total Subjects6
Raw Data AvailableYes
Raw Data File Type(s)cdf
Uploaded File Size830 M
Analysis Type DetailGC-MS
Release Date2014-11-06
Release Version1
Mona ElBadawi-Sidhu Mona ElBadawi-Sidhu application/zip

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Project ID:PR000106
Project DOI:doi: 10.21228/M8RC75
Project Title:Metabolomics analysis of multiple metabolic functions in the YjgF/YER057c/UK114 (Rid) protein family
Institute:University of California, Davis
Department:Genome Center
Laboratory:Fiehn Laboratory
Last Name:Fiehn
First Name:Oliver
Address:451 Health Sciences Drive, Davis, California 95616, USA
Funding Source:U.S. National Science Foundation award MCB-1153413


Subject ID:SU000136
Subject Type:Bacterial cells
Subject Species:Salmonella enterica;Escherichia coli
Taxonomy ID:28901|562
Genotype Strain:DM3480|DM14100|Salmonella enterica subsp.enterica serovar Typhimurium str.LT2|K12MG1655| ridA3::MudJ|ridA3::tn10ΔyoaB624::catSTM1549-26::kan| | |yjeF::kan
Species Group:Microorganism


Subject type: Bacterial cells; Subject species: Salmonella enterica;Escherichia coli (Factor headings shown in green)

mb_sample_id local_sample_id genotype
SA006164140826bmssa09_1single RidA knockout
SA006165140826bmssa07_1single RidA knockout
SA006166140826bmssa06_1single RidA knockout
SA006167140826bmssa10_1single RidA knockout
SA006168140826bmssa16_1single RidA knockout
SA006169140826bmssa03_1single RidA knockout
SA006170140826bmssa01_1triple RidA knockout
SA006171140826bmssa15_1triple RidA knockout
SA006172140826bmssa05_1triple RidA knockout
SA006173140826bmssa17_1triple RidA knockout
SA006174140826bmssa04_1triple RidA knockout
SA006175140826bmssa18_1triple RidA knockout
SA006158140826bmssa13_1Wild Type
SA006159140826bmssa11_1Wild Type
SA006160140826bmssa08_1Wild Type
SA006161140826bmssa02_1Wild Type
SA006162140826bmssa14_1Wild Type
SA006163140826bmssa12_1Wild Type
Showing results 1 to 18 of 18


Collection ID:CO000120
Sample Type:Bacterial Cells
Collection Method:6 independent colonies of each cell line were grown in M9 minimal medium at 37C until OD600 reached 1.5-2.0. An equivalent of 1 mL at OD 2.0 was placed into a 1.5 mL Eppi tube and spun for 15 sec. After removal of a 0.5 mL medium aliquot, remaining medium was removed and cell pellet was frozen in liquid nitrogen.
Collection Location:University of Florida, Gainesville
Collection Vials:1.5 mL eppendorf tube
Storage Vials:1.5 mL eppendorf tube


Treatment ID:TR000138

Sample Preparation:

Sampleprep ID:SP000133
Extraction Method:1 mL of cold, degassed extraction solvent (3:3:2 acetonitrile:isopropanol:water v/v/v) was added to each sample, vortexed for 10 seconds, then shaken at 4C for 4 min. Samples were spun down using a centrifuge at 14 rcf for 2 min. Aliquots (450 uL) were transferred to 1.5 mL eppendorf tubes and dried down using a Labconco centrivap evaporator.
Extract Storage:-80C
Sample Derivatization:10 uL of 40 mg/mL methoxyamine hydrochloride in pyridine was added to room temperature samples and shaken for 90 min at 30C. 91 uL of silyating agent (MSTFA) containing a set of 13 C8 - C30 fatty acid methyl ester internal standards was added and samples were shaken for 30 min at 37C. Derivatized samples were transferred to glass vials with inserts for analysis.
Sample Spiking:Set of 13 C8 - C30 fatty acid methyl esters (FAMES)

Combined analysis:

Analysis ID AN000198
Analysis type MS
Chromatography type GC
Chromatography system Agilent 6890N
Column Restek corporation Rtx-5Sil MS
MS Type EI
MS instrument type GC-TOF
MS instrument name Leco Pegasus III GC TOF
Units Peak area


Chromatography ID:CH000131
Chromatography Summary:Untargeted GC MS
Methods Filename:Data_Dictionary_Fiehn_laboratory_GCTOF_MS_primary_metabolism_09-27-2013_general.pdf
Instrument Name:Agilent 6890N
Column Name:Restek corporation Rtx-5Sil MS
Column Temperature:50-330oC
Flow Rate:1ml/min
Internal Standard:fatty acid methyl esters
Sample Injection:0.5uL
Oven Temperature:50C for 1 min, then ramped at 20C min-1 to 330C, held constant for 5 min
Transferline Temperature:280C
Washing Buffer:Ethyl Acetate
Sample Loop Size:30 m length x 0.25 mm internal diameter
Randomization Order:Excel generated
Chromatography Type:GC


MS ID:MS000161
Analysis ID:AN000198
Instrument Name:Leco Pegasus III GC TOF
Instrument Type:GC-TOF
MS Type:EI
Ion Source Temperature:250°C
Ionization:Electron Ionization (EI)
Ionization Energy:-70eV
Mass Accuracy:Nominal
Scanning Range:85-500 Da
Acquisition Parameters File:Data_Dictionary_Fiehn_laboratory_GCTOF_MS_primary_metabolism_09-27-2013_general.pdf
Processing Parameters File:Data_Dictionary_Fiehn_laboratory_GCTOF_MS_primary_metabolism_09-27-2013_general.pdf