Summary of study ST000118

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 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 IDST000118
Study TitleMetabolomics analysis of multiple metabolic functions in the YjgF/YER057c/UK114 (Rid) protein family GCMS (part 2)
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
Institute
University of California, Davis
DepartmentGenome Center
LaboratoryFiehn Laboratory
Last NameElBadawi-Sidhu
First NameMona
Address451 Health Sciences Drive, Davis, California 95616, USA
Emailmmelbadawi@ucdavis.edu
Submit Date2014-11-06
Num Groups5
Total Subjects6
Study CommentsOne sample missing (A6)
Raw Data AvailableYes
Raw Data File Type(s).peG,.cdf
Uploaded File Size611 M
Analysis Type DetailGC-MS
Release Date2014-11-06
Release Version1
Mona ElBadawi-Sidhu Mona ElBadawi-Sidhu
https://dx.doi.org/10.21228/M8RC75
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

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
Email:ofiehn@ucdavis.edu
Funding Source:U.S. National Science Foundation award MCB-1153413

Subject:

Subject ID:SU000137
Subject Type:Bacterial cells
Subject Species:Salmonella enterica/Escherichia coli
Genotype Strain:DM3480|DM14100|Salmonella enterica subsp. enterica serovar Typhimurium str. LT2|K 12 MG1655| ridA3::MudJ|ridA3::tn10 ?yoaB624::cat STM1549-26::kan| | |yjeF::kan
Species Group:Microorganism

Factors:

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

mb_sample_id local_sample_id Strain Genotype
SA006176140721bjlsa50_1E. coli WT E. coli
SA006177140721bjlsa05_1E. coli WT E. coli
SA006178140721bjlsa46_1E. coli WT E. coli
SA006179140721bjlsa42_1E. coli WT E. coli
SA006180140722bjlsa07_1E. coli WT E. coli
SA006181140721bjlsa36_1E. coli yjeF KO
SA006182140721bjlsa03_1E. coli yjeF KO
SA006183140721bjlsa08_1E. coli yjeF KO
SA006184140721bjlsa12_1E. coli yjeF KO
SA006185140721bjlsa38_1E. coli yjeF KO
SA006186140721bjlsa34_1E. coli yjeF KO
SA006193140721bjlsa33_1S. enterica single RidA KO
SA006194140722bjlsa06_1S. enterica single RidA KO
SA006195140721bjlsa47_1S. enterica single RidA KO
SA006196140721bjlsa21_1S. enterica single RidA KO
SA006197140721bjlsa19_1S. enterica single RidA KO
SA006198140721bjlsa09_1S. enterica single RidA KO
SA006199140721bjlsa23_1S. enterica triple RidA KO
SA006200140722bjlsa10_1S. enterica triple RidA KO
SA006201140721bjlsa15_1S. enterica triple RidA KO
SA006202140721bjlsa17_1S. enterica triple RidA KO
SA006203140721bjlsa44_1S. enterica triple RidA KO
SA006204140722bjlsa04_1S. enterica triple RidA KO
SA006187140721bjlsa06_1S. enterica WT S. enterica
SA006188140721bjlsa22_1S. enterica WT S. enterica
SA006189140722bjlsa02_1S. enterica WT S. enterica
SA006190140721bjlsa24_1S. enterica WT S. enterica
SA006191140721bjlsa25_1S. enterica WT S. enterica
SA006192140721bjlsa45_1S. enterica WT S. enterica
Showing results 1 to 29 of 29

Collection:

Collection ID:CO000121
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:

Treatment ID:TR000139

Sample Preparation:

Sampleprep ID:SP000134
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 AN000199
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
Ion Mode POSITIVE
Units Peak area

Chromatography:

Chromatography ID:CH000132
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:

MS ID:MS000162
Analysis ID:AN000199
Instrument Name:Leco Pegasus III GC TOF
Instrument Type:GC-TOF
MS Type:EI
Ion Mode:POSITIVE
Ion Source Temperature:250°C
Ionization:Electron Ionization (EI)
Ionization Energy:-70eV
Mass Accuracy:Nominal
Scanning Range:85-500 Da
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