Metabolomics Workbench : NIH Data Repository

MB Sample ID: SA094375

Local Sample ID:	RidA5
Subject ID:	SU001379
Subject Type:	Bacteria
Subject Species:	Salmonella enterica
Taxonomy ID:	28901
Species Group:	Bacteria

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Subject:

Subject ID:	SU001379
Subject Type:	Bacteria
Subject Species:	Salmonella enterica
Taxonomy ID:	28901
Species Group:	Bacteria

Factors:

Local Sample ID	MB Sample ID	Factor Level ID	Level Value	Factor Name
RidA5	SA094375	FL013484	RidA KO	Strain

Collection:

Collection ID:	CO001374
Collection Summary:	Ten biologically independent cultures each of wild-type (DM9404) and ridA mutant (DM3480) strains were grown overnight in NB medium at 37 °C and used to inoculate (1% inoculum) 250 mL minimal glucose medium in 500 mL non-baffled flasks. Flasks were randomly arranged in an Innova®44 incubator and cultures were allowed to grow 16 h shaking at 180 RPM and 37 °C. Cultures were cooled on ice 5 min and then harvested by centrifugation at 7,000 x G for 10 min at 4 °C. The supernatant was decanted, pellets were resuspended in 10 mL ddH2O and transferred to sterile 15 mL conical tubes in which they were pelleted at 7,000 x G 10 min at 4 °C. Final supernatant was decanted and pellets were frozen in liquid nitrogen and stored at -80 °C prior to cell extractions.
Sample Type:	Bacterial cells
Storage Conditions:	-80℃

Treatment:

Treatment ID:	TR001394
Treatment Summary:	These samples did not undergo addition treatment.

Sample Preparation:

Sampleprep ID:	SP001387
Sampleprep Summary:	Each frozen bacterial pellet (~1 g) was thawed on ice and homogenized 3 times. For homogenization, 2.6 g of 0.1 mm zirconium beads and 6 mL 4 C MeOH/H2O (80/20) solvent was added and samples were agitated 7 times (210 s total) at 1600 rpm in a FastPrep 96 (MPBIO). Samples were then centrifuged at 416 g and 4 C for 16 min and supernatant was transferred to a new 15 mL conical tube. Homogenization was carried out a second and third time using 4 mL MeOH/H2O with 4 homogenization cycles (150 s) and 2 mL MeOH/H2O with 3 homogenization cycles (150 s), respectively. Pooled supernatants from each sample were concentrated to dryness using a CentriVap Benchtop Vacuum Concentrator (Labconco). The extracts were reconstituted in 600 L of deuterated 100 mM sodium phosphate buer (pH 7.4) containing 1 mM of the internal standard DSS (d6 4,4-dimethyl-4-silapentane-1-sulfonic acid) and vortex mixed 2 min. Each sample was transferred into 5 mm SampleJet NMR tubes for NMR analysis.

Sampleprep ID:

SP001387

Sampleprep Summary:

Each frozen bacterial pellet (~1 g) was thawed on ice and homogenized 3 times. For homogenization, 2.6 g of 0.1 mm zirconium beads and 6 mL 4 C MeOH/H2O (80/20) solvent was added and samples were agitated 7 times (210 s total) at 1600 rpm in a FastPrep 96 (MPBIO). Samples were then centrifuged at 416 g and 4 C for 16 min and supernatant was transferred to a new 15 mL conical tube. Homogenization was carried out a second and third time using 4 mL MeOH/H2O with 4 homogenization cycles (150 s) and 2 mL MeOH/H2O with 3 homogenization cycles (150 s), respectively. Pooled supernatants from each sample were concentrated to dryness using a CentriVap Benchtop Vacuum Concentrator (Labconco). The extracts were reconstituted in 600 L of deuterated 100 mM sodium phosphate buer (pH 7.4) containing 1 mM of the internal standard DSS (d6 4,4-dimethyl-4-silapentane-1-sulfonic acid) and vortex mixed 2 min. Each sample was transferred into 5 mm SampleJet NMR tubes for NMR analysis.

Analysis:

MB Sample ID:	SA094375
Analysis ID:	AN002174
Laboratory Name:	Complex Carbohydrate Research Center NMR Facility
Analysis Type:	NMR
Operator Name:	Adrien Le Guennec
Num Factors:	2
Num Metabolites:	37
Units:	Area Under Curve

NMR:

NMR ID:	NM000159
Analysis ID:	AN002174
Instrument Name:	Bruker Avance III HD
Instrument Type:	FT-NMR
NMR Experiment Type:	1D-1H
Spectrometer Frequency:	800 MHz