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MB Sample ID: SA091500

Local Sample ID:Fn_2
Subject ID:SU001328
Subject Type:Bacteria
Subject Species:Fusobacterium nucleatum subsp. nucleatum ATCC 25586
Taxonomy ID:190304
Genotype Strain:ATCC 25586
Cell Biosource Or Supplier:ATCC 25586

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Subject:

Subject ID:SU001328
Subject Type:Bacteria
Subject Species:Fusobacterium nucleatum subsp. nucleatum ATCC 25586
Taxonomy ID:190304
Genotype Strain:ATCC 25586
Cell Biosource Or Supplier:ATCC 25586

Factors:

Local Sample IDMB Sample IDFactor Level IDLevel ValueFactor Name
Fn_2SA091500FL013180nonepartner

Collection:

Collection ID:CO001322
Collection Summary:After 6 h of co-culture, F. nucleatum cells were collected by pipetting from the lower chamber and washed with Milli-Q water by centrifugation. Bacterial pellets were immediately fixed by adding methanol containing 5 µM internal standard.
Sample Type:Bacterial cells

Treatment:

Treatment ID:TR001343
Treatment Summary:Co-culture growth was performed by inoculating 1.4E+10 cells of F. nucleatum in CDM in the lower chamber of a Transwell unit with 0.4-µm pore polystyrene membrane inserts (Corning, NY, USA), into which 1.4E+10 cells of S. gordonii, V. parvula or their mixture (7E+9 cells each) in CDM, or an equal volume of CDM (as a control) were added. The setup was anaerobically incubated in triplicate for 37°C.

Sample Preparation:

Sampleprep ID:SP001336
Sampleprep Summary:To remove protein, 2 ml of chloroform and 0.8 ml of ultrapure water were added to the samples, which were thoroughly mixed and centrifuged at 2300 × g for 5 minutes at 4˚C. The upper aqueous layer was then transferred to ultrafilter tips (Amicon ultrafilter system™) and centrifuged at 9100 × g for 120 minutes at 4˚C. Filtered material was dried under reduced pressure, followed by suspension in 50 µl of ultrapure water.

Combined analysis:

Analysis ID AN002090 AN002091
Analysis type MS MS
Chromatography type CE CE
Chromatography system Agilent 6210 Agilent 6210
Column None None
MS Type ESI ESI
MS instrument type CE-TOF CE-TOF
MS instrument name Agilent 6210 TOF Agilent 6210 TOF
Ion Mode POSITIVE NEGATIVE
Units AU AU

Chromatography:

Chromatography ID:CH001527
Instrument Name:Agilent 6210
Column Name:None
Chromatography Type:CE

MS:

MS ID:MS001941
Analysis ID:AN002090
Instrument Name:Agilent 6210 TOF
Instrument Type:CE-TOF
MS Type:ESI
MS Comments:The conditions for measurement of cationic metabolites were as follows. Run buffer: Cation Buffer Solution (H3301-1001; Human Metabolome Technologies (HMT)), CE voltage: +27kV, MS ionization: ESI positive, MS capillary voltage: 4,000V, MS scan range: m/z 50-1,000, and sheath liquid: HMT Sheath Liquid (H3301-1020). Identification of metabolites and evaluation of the relative amounts were conducted using Master Hands (version 2.16.0.15 and 2.17.1.11; Keio University, Tokyo, Japan) with the HMT metabolite database. The relative amount of each metabolite was calculated with reference to the internal standard material (HMT).
Ion Mode:POSITIVE
  
MS ID:MS001942
Analysis ID:AN002091
Instrument Name:Agilent 6210 TOF
Instrument Type:CE-TOF
MS Type:ESI
MS Comments:The conditions for measurement of anionic metabolites were as follows. Run buffer: Anion Buffer Solution (H3302-1023), CE voltage: +30kV, MS ionization: ESI negative, MS capillary voltage: 3,500V, MS scan range: m/z 50-1,000, and sheath liquid: HMT Sheath Liquid (H3301-1020). Identification of metabolites and evaluation of the relative amounts were conducted using Master Hands (version 2.16.0.15 and 2.17.1.11; Keio University, Tokyo, Japan) with the HMT metabolite database. The relative amount of each metabolite was calculated with reference to the internal standard material (HMT).
Ion Mode:NEGATIVE
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