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MB Sample ID: SA091499
Local Sample ID: | Fn-Vp_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 |
Select appropriate tab below to view additional metadata details:
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 ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
---|---|---|---|---|
Fn-Vp_2 | SA091499 | FL013179 | Vp | partner |
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 |