Summary of Study ST000119

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 IDST000119
Study TitleMetabolomics analysis of multiple metabolic functions in the YjgF/YER057c/UK114 (Rid) protein family LCMS
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 and Biomedical Sciences Facility
LaboratoryFiehn Laboratory
Last NameElBadawi-Sidhu
First NameMona
Address451 Health Sciences Drive, Davis, California 95616, USA
Emailmmelbadawi@ucdavis.edu
Submit Date2014-11-06
Num Groups4
Total Subjects6
Study CommentsSamples were measured in poitive and negative ionization mode. MS/MS files contain product ion scans (MS/MS) spectra for compound identification.
Raw Data AvailableNo
Raw Data File Type(s)d
Analysis Type DetailLC-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:SU000138
Subject Type:Bacterial cells
Subject Species:Salmonella enterica;Escherichia coli
Taxonomy ID:28901|562
Genotype Strain:DM14100|Salmonella enterica subsp. enterica serovar Typhimurium str. LT2|K 12 MG1655|K 12 MG1655 ridA3::tn10 ΔyoaB624::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
SA006213041113_EcoliCells_WT_R1_0005E.coli Wild-type
SA006214041113_EcoliCells_WT_R2_0060E.coli Wild-type
SA006215041113_EcoliCells_WT_Pool_MSMS_0064E.coli Wild-type
SA006216041113_EcoliCells_WT_R3_0044E.coli Wild-type
SA006217041113_EcoliCells_WT_R4_0034E.coli Wild-type
SA006218041113_EcoliCells_WT_R6_0023E.coli Wild-type
SA006219041113_EcoliCells_WT_R5_0037E.coli Wild-type
SA006206041113_EcoliCells_Yjef_R4_0038E.coli Δyjef Knock-out
SA006207041113_EcoliCells_Yjef_R5_0042E.coli Δyjef Knock-out
SA006208041113_EcoliCells_Yjef_R6_0025E.coli Δyjef Knock-out
SA006209041113_EcoliCells_Yjef_R2_0059E.coli Δyjef Knock-out
SA006210041113_EcoliCells_Yjef_Pool_MSMS_0066E.coli Δyjef Knock-out
SA006211041113_EcoliCells_Yjef_R3_0011E.coli Δyjef Knock-out
SA006212041113_EcoliCells_Yjef_R1_0049E.coli Δyjef Knock-out
SA006220041213_SentericaCells_RidAKO_R6_0055S.enterica RidA Knock-out
SA006221041113_SentericaCells_RidAKO_Pool_MSMS_0070S.enterica RidA Knock-out
SA006222041213_SentericaCells_RidAKO_R3_0029S.enterica RidA Knock-out
SA006223041213_SentericaCells_RidAKO_R4_0057S.enterica RidA Knock-out
SA006224041213_SentericaCells_RidAKO_R5_0035S.enterica RidA Knock-out
SA006225041213_SentericaCells_RidAKO_R2_0047S.enterica RidA Knock-out
SA006226041213_SentericaCells_RidAKO_R1_0022S.enterica RidA Knock-out
SA006227041113_SentericaCells_WT_Pool_MSMS_0068S.enterica Wild-type
SA006228041213_SentericaCells_WT_R6_0050S.enterica Wild-type
SA006229041213_SentericaCells_WT_R2_0058S.enterica Wild-type
SA006230041213_SentericaCells_WT_R3_0043S.enterica Wild-type
SA006231041213_SentericaCells_WT_R4_0021S.enterica Wild-type
SA006232041213_SentericaCells_WT_R5_0019S.enterica Wild-type
SA006233041213_SentericaCells_WT_R1_0048S.enterica Wild-type
Showing results 1 to 28 of 28

Collection:

Collection ID:CO000122
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:TR000140

Sample Preparation:

Sampleprep ID:SP000135
Sampleprep Summary:-
Processing Storage Conditions:on ice
Extraction Method:1.1 mL of cold, degassed extraction solvent (3:1 Methanol:Water) was added to each sample. Samples were vortexed for 20 sec then placed in sonicator for 5 min, followed by another 20 sec vortex. Samples were placed in -20C for 30 minutes prior to spinning down in centrifuge at 14 rcf for 5 min. The supernatant was transferred to 1.5 mL eppendorf tubes and evaporated in the Labconco speed vac.
Extract Storage:-80C
Sample Resuspension:H20 + 5mM NH4OAc + 0.2% Acetic Acid

Combined analysis:

Analysis ID AN000200 AN000201
Analysis type MS MS
Chromatography type HILIC HILIC
Chromatography system Agilent 1290 Agilent 1290
Column Waters Acquity BEH Amide (150 x 2.1mm,1.7um) Waters Acquity BEH Amide (150 x 2.1mm,1.7um)
MS Type ESI ESI
MS instrument type QTOF QTOF
MS instrument name Agilent 6530 QTOF Agilent 6530 QTOF
Ion Mode POSITIVE NEGATIVE
Units Peak area Peak area

Chromatography:

Chromatography ID:CH000133
Chromatography Summary:Untargeted LC MS
Instrument Name:Agilent 1290
Column Name:Waters Acquity BEH Amide (150 x 2.1mm,1.7um)
Column Pressure:300 bar (max)
Column Temperature:40 C
Flow Gradient:0 - 4 min: 0% B; 4-12 min: linear gradient to 45% B; 12-20 min: 45% B
Flow Rate:0.25 mL/min
Injection Temperature:4C
Sample Injection:5 uL
Solvent A:100% water; 0.2% acetic acid; 5mM ammonium acetate
Solvent B:90% acetonitrile/10% water; 0.2% acetic acid; 5 mM ammonium acetate
Oven Temperature:H20 + 5mM NH4OAc + 0.2% Acetic Acid
Time Program:20 min
Weak Wash Solvent Name:50:50 Methanol:Water
Weak Wash Volume:15 seconds
Target Sample Temperature:Autosampler temperature 4C
Randomization Order:Excel generated
Chromatography Type:HILIC

MS:

MS ID:MS000163
Analysis ID:AN000200
Instrument Name:Agilent 6530 QTOF
Instrument Type:QTOF
MS Type:ESI
Ion Mode:POSITIVE
Capillary Voltage:3000
Collision Energy:Ramped 0.02eV/m/z + 10 eV
Collision Gas:Nitrogen
Dry Gas Flow:Nebulizer: 10 L/min Sheath: 9 L/min
Dry Gas Temp:Nebulizer and Sheath: 350
Fragment Voltage:125
Ionization:Positive
Precursor Type:Intact Molecule
Reagent Gas:Nitrogen
Dataformat:.d
Nebulizer:35 psig
Octpole Voltage:750
Resolution Setting:Extended Dynamic Range
Scan Range Moverz:100 - 1700 m/z
Scanning Cycle:2
  
MS ID:MS000164
Analysis ID:AN000201
Instrument Name:Agilent 6530 QTOF
Instrument Type:QTOF
MS Type:ESI
Ion Mode:NEGATIVE
Capillary Voltage:3000
Collision Energy:Ramped 0.02eV/m/z + 10 eV
Collision Gas:Nitrogen
Dry Gas Flow:Nebulizer: 10 L/min Sheath: 9 L/min
Dry Gas Temp:Nebulizer and Sheath: 350
Fragment Voltage:125
Ionization:Negative
Precursor Type:Intact Molecule
Reagent Gas:Nitrogen
Dataformat:.d
Nebulizer:35 psig
Octpole Voltage:750
Resolution Setting:Extended Dynamic Range
Scan Range Moverz:100 - 1700 m/z
Scanning Cycle:2
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