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MB Sample ID: SA011859
| Local Sample ID: | WT_M4c |
| Subject ID: | SU000278 |
| Subject Type: | Bacterial cells |
| Subject Species: | Sinorhizobium meliloti |
| Taxonomy ID: | 382 |
| Genotype Strain: | Rm2011 (SU47 str-3)|SmA818|RmP3009|RmP2917 |
| Human Ethnicity: | wild type|Rm2011 lack pSymA|Rm2011 lack pSymB|Rm2011 lack pSymA and pSymB | a tRNAarg and the smb20996-engA operon from pSymB were integrated to chromosome in strains RmP3009 and RmP2917 |
| Species Group: | Bacteria |
Select appropriate tab below to view additional metadata details:
Subject:
| Subject ID: | SU000278 |
| Subject Type: | Bacterial cells |
| Subject Species: | Sinorhizobium meliloti |
| Taxonomy ID: | 382 |
| Genotype Strain: | Rm2011 (SU47 str-3)|SmA818|RmP3009|RmP2917 |
| Human Ethnicity: | wild type|Rm2011 lack pSymA|Rm2011 lack pSymB|Rm2011 lack pSymA and pSymB | a tRNAarg and the smb20996-engA operon from pSymB were integrated to chromosome in strains RmP3009 and RmP2917 |
| Species Group: | Bacteria |
Factors:
| Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
|---|---|---|---|---|
| WT_M4c | SA011859 | FL002931 | wild type | strains |
Collection:
| Collection ID: | CO000271 |
| Collection Summary: | - |
| Sample Type: | cells |
| Volumeoramount Collected: | 6 x 108 cells |
| Storage Conditions: | -80ºC freezer |
| Collection Vials: | eppendorf tube |
| Tissue Cell Identification: | 6 x 108 cells |
Treatment:
| Treatment ID: | TR000291 |
| Animal Vet Treatments: | -80ºC freezer |
| Animal Anesthesia: | test tube |
| Animal Endp Tissue Proc Method: | M9 miminal medium plus 10 mM sucrose |
| Animal Endp Clinical Signs: | n/a |
| Human Fasting: | 30ºC incubator |
| Human Endp Clinical Signs: | OD600 values of approximately 0.3, 0.5, 0.9, 1.6, and 3.5 (except for Rm2011 which reached ~4.8) |
Sample Preparation:
| Sampleprep ID: | SP000285 |
| Sampleprep Summary: | - |
| Sampleprep Protocol Filename: | Fei,_F.,_Bowdish,_D._M._E.,_&_McCarry,_B._E._(2014)._Analytical_and_Bioanalytical_Chemistry,_406,_37233733. |
| Extraction Method: | cell pellet extracted with 2:2:1 MeOH/EtOH/H2O with beadbeating |
| Extract Storage: | -80ºC freezer |
| Sample Resuspension: | cell extracts suspended 60%v/v acetonitrile/water |
| Sample Spiking: | L-methionine-d3, L-tryptophan-d5 as standards for recovery determination ; L-phenylalanine-d8, diphenylalanine and glycine-phenylalanine as internal standards for peak area normalization |
| Cell Type: | Gram negative bacterium |
Combined analysis:
| Analysis ID | AN000409 | AN000410 |
|---|---|---|
| Chromatography ID | CH000290 | CH000290 |
| MS ID | MS000351 | MS000352 |
| Analysis type | MS | MS |
| Chromatography type | HILIC | HILIC |
| Chromatography system | Agilent 1200 RR Series II | Agilent 1200 RR Series II |
| Column | Phenomenex Kinetex HILIC 100A (50 x 2.1 mm,2.6um) | Phenomenex Kinetex HILIC 100A (50 x 2.1 mm,2.6um) |
| MS Type | ESI | ESI |
| MS instrument type | QTOF | QTOF |
| MS instrument name | Bruker MicrOTOF II | Bruker MicrOTOF II |
| Ion Mode | POSITIVE | NEGATIVE |
| Units | normalized peak area | normalized peak area |
Chromatography:
| Chromatography ID: | CH000290 |
| Methods Filename: | Opt_silicaHILIC.m |
| Instrument Name: | Agilent 1200 RR Series II |
| Column Name: | Phenomenex Kinetex HILIC 100A (50 x 2.1 mm,2.6um) |
| Column Temperature: | 40C |
| Flow Gradient: | 0-0.5 min, 95%A; 0.5-12.5 min, 35%A; 12.5-13.0 min, 35%A; 13.0-14.0 min, 95%A; 14.0-24.0 min, 95%A |
| Flow Rate: | 200 ?L/min |
| Internal Standard: | L-phenylalanine-d8, diphenylalanine and glycine-phenylalanine |
| Sample Injection: | 2 ?L |
| Solvent A: | 100% acetonitrile |
| Solvent B: | 100% water;10 mM ammonium acetate, adjust to pH 3 with formic acid |
| Analytical Time: | 24 min |
| Chromatography Type: | HILIC |
MS:
| MS ID: | MS000351 |
| Analysis ID: | AN000409 |
| Instrument Name: | Bruker MicrOTOF II |
| Instrument Type: | QTOF |
| MS Type: | ESI |
| Ion Mode: | POSITIVE |
| Capillary Voltage: | -3800 V |
| Dry Gas Flow: | 8.0 L/min |
| Dry Gas Temp: | 250ºC |
| Scan Range Moverz: | 50-1000 m/z |
| MS ID: | MS000352 |
| Analysis ID: | AN000410 |
| Instrument Name: | Bruker MicrOTOF II |
| Instrument Type: | QTOF |
| MS Type: | ESI |
| Ion Mode: | NEGATIVE |
| Capillary Voltage: | 4500 V |
| Dry Gas Flow: | 8.0 L/min |
| Dry Gas Temp: | 250ºC |
| Scan Range Moverz: | 50-1000 m/z |
