Summary of Study ST000117
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.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
Study ID | ST000117 |
Study Title | Metabolomics analysis of multiple metabolic functions in the YjgF/YER057c/UK114 (Rid) protein family GC-MS (Part 1) |
Study Type | wildtype vs knock-out |
Study Summary | Metabolomics 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 |
Department | Genome Center |
Laboratory | Fiehn Laboratory |
Last Name | ElBadawi-Sidhu |
First Name | Mona |
Address | 451 Health Sciences Drive, Davis, California 95616, USA |
mmelbadawi@ucdavis.edu | |
Submit Date | 2014-11-06 |
Num Groups | 3 |
Total Subjects | 6 |
Raw Data Available | Yes |
Raw Data File Type(s) | cdf |
Uploaded File Size | 830 M |
Analysis Type Detail | GC-MS |
Release Date | 2014-11-06 |
Release Version | 1 |
Select appropriate tab below to view additional metadata details:
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: | 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: | Bacteria |
Factors:
Subject type: Bacterial cells; Subject species: Salmonella enterica;Escherichia coli (Factor headings shown in green)
mb_sample_id | local_sample_id | genotype |
---|---|---|
SA006164 | 140826bmssa09_1 | single RidA knockout |
SA006165 | 140826bmssa07_1 | single RidA knockout |
SA006166 | 140826bmssa06_1 | single RidA knockout |
SA006167 | 140826bmssa10_1 | single RidA knockout |
SA006168 | 140826bmssa16_1 | single RidA knockout |
SA006169 | 140826bmssa03_1 | single RidA knockout |
SA006170 | 140826bmssa01_1 | triple RidA knockout |
SA006171 | 140826bmssa15_1 | triple RidA knockout |
SA006172 | 140826bmssa05_1 | triple RidA knockout |
SA006173 | 140826bmssa17_1 | triple RidA knockout |
SA006174 | 140826bmssa04_1 | triple RidA knockout |
SA006175 | 140826bmssa18_1 | triple RidA knockout |
SA006158 | 140826bmssa13_1 | Wild Type |
SA006159 | 140826bmssa11_1 | Wild Type |
SA006160 | 140826bmssa08_1 | Wild Type |
SA006161 | 140826bmssa02_1 | Wild Type |
SA006162 | 140826bmssa14_1 | Wild Type |
SA006163 | 140826bmssa12_1 | Wild Type |
Showing results 1 to 18 of 18 |
Collection:
Collection ID: | CO000120 |
Collection Summary: | - |
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: | TR000138 |
Sample Preparation:
Sampleprep ID: | SP000133 |
Sampleprep Summary: | - |
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 |
Ion Mode | POSITIVE |
Units | Peak area |
Chromatography:
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:
MS ID: | MS000161 |
Analysis ID: | AN000198 |
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 |
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 |