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MB Sample ID: SA011357
| Local Sample ID: | 6C |
| Subject ID: | SU000267 |
| Subject Type: | Bacterial cells |
| Subject Species: | Staphylococcus aureus |
| Taxonomy ID: | 1280 |
| Species Group: | Microorganism |
Select appropriate tab below to view additional metadata details:
Subject:
| Subject ID: | SU000267 |
| Subject Type: | Bacterial cells |
| Subject Species: | Staphylococcus aureus |
| Taxonomy ID: | 1280 |
| Species Group: | Microorganism |
Factors:
| Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
|---|---|---|---|---|
| 6C | SA011357 | FL002841 | nos SrrAB mutant nos complement | Strain |
| 6C | SA011357 | FL002841 | Whole Cells | Sample type |
Collection:
| Collection ID: | CO000258 |
| Collection Summary: | The wildtype S. aureus, nos mutant, SrrAB mutant, nos SrrAB double mutant, and complement strains will be grown in 40 ml trytic soy broth lacking dextrose for 4 hours. At 4 hours growth, all 40 ml was isolated, centrifuged at 4500 rpms and 4C for 10 minutes and then placed on ice. 1 ml of supernatant was removed in duplicate and saved as supernatant. The rest of the supernatant was discarded and pellets were resuspended in 2 ml PBS, centrifuged at 4500 rpms for 3 minutes (4C). Supernatant was discarded and samples were again resuspended in 2 ml PBS. These samples were split into 2 separate 1 ml aliquots (for metabolite and protein determination) and frozen with liquid nitrogen. Separate media only samples of Tryptic Soy Broth without dextrose were isolated for each day (3 total) Samples were stored at -80C. A total of 39 samples (18 whole cell, 18 supernatant, and 3 media) were isolated. |
| Collection Protocol Filename: | Rice_Collections_targeted_20150807.txt |
| Sample Type: | Bacterial cells |
Treatment:
| Treatment ID: | TR000278 |
| Treatment Summary: | nos mutation, SrrAB mutation, and nos SrrAB double mutant mutations were completed; as well as complementation before growing each strain under the same conditions. All strains were grown in Tryptic soy broth without dextrose. No additional treatment and/or variables are included in the experiment. |
| Treatment Protocol Filename: | Rice_Treatments_targeted_20150807.txt |
Sample Preparation:
| Sampleprep ID: | SP000272 |
| Sampleprep Summary: | Amino acid|Organic acid|NAD|NADH |
| Sampleprep Protocol Filename: | SB_AA_Assay.pdf SB_OA_Assay.pdf SB_NAD_Assay.pdf SB_NADH_Assay.pdf |
Combined analysis:
| Analysis ID | AN000387 | AN000388 | AN000389 | AN000390 |
|---|---|---|---|---|
| Analysis type | MS | MS | MS | MS |
| Chromatography type | Reversed phase | Reversed phase | Reversed phase | Reversed phase |
| Chromatography system | Thermo Dionex Ultimate 3000 | Thermo Dionex Ultimate 3000 | Thermo Dionex Ultimate 3000 | Agilent 1290 Infinity |
| Column | Waters Acquity BEH C18 (100 x 2mm,1.7um) | Thermo Hypercarb (50 x 2.1mm,3um) | Waters Acquity HSS T3 (100 x 2.1mm,1.8um) | Waters AccQ Tag (100 x 2mm,1.7um) |
| MS Type | ESI | ESI | ESI | ESI |
| MS instrument type | Triple quadrupole | Triple quadrupole | Triple quadrupole | Triple quadrupole |
| MS instrument name | Thermo Quantiva QQQ | Thermo Quantiva QQQ | Thermo Quantiva QQQ | Agilent 6490 QQQ |
| Ion Mode | POSITIVE | POSITIVE | POSITIVE | POSITIVE |
| Units | nmol/mg protein | nmol/mg protein | nmol/mg protein | nmol/mg protein |
Chromatography:
| Chromatography ID: | CH001331 |
| Methods Filename: | SB_OA_Assay.pdf |
| Instrument Name: | Thermo Dionex Ultimate 3000 |
| Column Name: | Waters Acquity BEH C18 (100 x 2mm,1.7um) |
| Column Temperature: | 45 |
| Flow Rate: | 0.3 mL/min |
| Solvent A: | 100% water; 0.1% formic acid |
| Solvent B: | 100% acetonitrile; 0.1% formic acid |
| Chromatography Type: | Reversed phase |
| Chromatography ID: | CH001332 |
| Methods Filename: | SB_NAD_Assay.pdf |
| Instrument Name: | Thermo Dionex Ultimate 3000 |
| Column Name: | Thermo Hypercarb (50 x 2.1mm,3um) |
| Column Temperature: | 30 |
| Flow Rate: | 0.65 mL/min |
| Solvent A: | 100% water; 10 mM ammonium acetate, pH 9.5 |
| Solvent B: | 100% acetonitrile |
| Chromatography Type: | Reversed phase |
| Chromatography ID: | CH001333 |
| Methods Filename: | SB_NADH_Assay.pdf |
| Instrument Name: | Thermo Dionex Ultimate 3000 |
| Column Name: | Waters Acquity HSS T3 (100 x 2.1mm,1.8um) |
| Chromatography Type: | Reversed phase |
| Chromatography ID: | CH001334 |
| Methods Filename: | SB_AA_Assay.pdf |
| Instrument Name: | Agilent 1290 Infinity |
| Column Name: | Waters AccQ Tag (100 x 2mm,1.7um) |
| Column Temperature: | 55 |
| Flow Rate: | 0.7 mL/min |
| Solvent A: | AccQ·Tag Eluent A |
| Solvent B: | accQ·Tag Eluent B |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS000331 |
| Analysis ID: | AN000387 |
| Instrument Name: | Thermo Quantiva QQQ |
| Instrument Type: | Triple quadrupole |
| MS Type: | ESI |
| MS Comments: | Organic Acids (Instrument:Thermo Scientific Quantiva) |
| Ion Mode: | POSITIVE |
| MS ID: | MS000332 |
| Analysis ID: | AN000388 |
| Instrument Name: | Thermo Quantiva QQQ |
| Instrument Type: | Triple quadrupole |
| MS Type: | ESI |
| MS Comments: | NAD(Instrument:Thermo Scientific Quantiva) |
| Ion Mode: | POSITIVE |
| MS ID: | MS000333 |
| Analysis ID: | AN000389 |
| Instrument Name: | Thermo Quantiva QQQ |
| Instrument Type: | Triple quadrupole |
| MS Type: | ESI |
| MS Comments: | NADH(Instrument:Thermo Scientific Quantiva) |
| Ion Mode: | POSITIVE |
| MS ID: | MS000334 |
| Analysis ID: | AN000390 |
| Instrument Name: | Agilent 6490 QQQ |
| Instrument Type: | Triple quadrupole |
| MS Type: | ESI |
| MS Comments: | Amino Acids(Instrument:Agilent 6490) |
| Ion Mode: | POSITIVE |
