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) |
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 |
Analysis:
| Analysis ID: | AN000198 |
| Laboratory Name: | Fiehn Laboratory |
| Analysis Type: | MS |
| Analysis Comments: | GCMS |
| Acquisition Date: | 07/2014 and 08/2014 |
| Acquisition Time: | 20 min |
| Acquisition Parameters File: | Data_Dictionary_Fiehn_laboratory_GCTOF_MS_primary_metabolism_09-27-2013_general.pdf |
| Instrument Name: | Leco Pegasus III GC-TOF |
| Software Version: | ChromaTOF |
| Processing Parameters File: | Data_Dictionary_Fiehn_laboratory_GCTOF_MS_primary_metabolism_09-27-2013_general.pdf |
| Randomization Order: | Excel generated |
| Detector Type: | TOF |
| Data Format: | .peg, .txt, .cdf |
| Chromatography ID: | CH000131 |
| Num Factors: | 3 |
| Num Metabolites: | 95 |
| Units: | Peak area |
