|
| Status |
Public on May 01, 2009 |
| Title |
Sm M95 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
Sm M95
|
| Organism |
Sinorhizobium meliloti |
| Characteristics |
strain: M95
type: Bacterium-natural strain
|
| Growth protocol |
To obtain genomic DNA for microarray analysis, cells of individual strains were inoculated into 5ml LBmc broth (LB supplemented with 2.5 mM MgSO4 and 2.5 mM CaCl2). The cells were incubated at 30oC with a constant agitation at 120rpm and harvested when the population density reached an OD600 reading between 0.8-1.0.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted by using the Wizard Genomic DNA purification kit (Promega, Madison, WI, USA # A1120) according to the protocols provided.
|
| Label |
Alexa555
|
| Label protocol |
Microarrays were hybridized using Pronto!™ Universal Hybridization Kits (Corning Incorporated, Life Sciences, Acton, USA Cat# 40026), following the protocol provided.
|
| |
|
| Channel 2 |
| Source name |
Sm 1021
|
| Organism |
Sinorhizobium meliloti |
| Characteristics |
strain: Rm1021
type: Bacterium-sequenced strain
|
| Growth protocol |
To obtain genomic DNA for microarray analysis, cells of individual strains were inoculated into 5ml LBmc broth (LB supplemented with 2.5 mM MgSO4 and 2.5 mM CaCl2). The cells were incubated at 30oC with a constant agitation at 120rpm and harvested when the population density reached an OD600 reading between 0.8-1.0.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted by using the Wizard Genomic DNA purification kit (Promega, Madison, WI, USA # A1120) according to the protocols provided.
|
| Label |
Alexa647
|
| Label protocol |
Microarrays were hybridized using Pronto!™ Universal Hybridization Kits (Corning Incorporated, Life Sciences, Acton, USA Cat# 40026), following the protocol provided.
|
| |
|
| |
| Hybridization protocol |
Two differentially labeled genomic DNA samples were included for each hybridization; the reference strain Rm1021 and another strain depending on the experiment. Thus, each hybridization reaction contained a 10 μl (equivalent 2μg DNA) of Alexa 555 and Alexa-647 labeled genomic DNA samples mixed in the hybridization solution (Pronto! Long Oligo/cDNA, 3x SSC, 0.1% SDS, 0.1 mg of sonicated Salmon Sperm DNA/ml) in a final volume of 70μl.
|
| Scan protocol |
Scanned on a ScanArrayExpress microarray scanner (Perkin-Elmer TM, Boston, MA, USA).
|
| Description |
none
|
| Data processing |
Spot quantification, signal normalization, and data visualization were performed with the ScanArray Express 3.0 software (Perkin-Elmer TM Instruments)
|
| |
|
| Submission date |
Apr 29, 2009 |
| Last update date |
Apr 30, 2009 |
| Contact name |
HONG GUO |
| Organization name |
MCMASTER UNIVERSITY
|
| Department |
BIOLOGY
|
| Lab |
DR.XU,JP
|
| Street address |
1280Main St. West
|
| City |
Hamilton |
| State/province |
Ontario |
| ZIP/Postal code |
L8S 4K1 |
| Country |
Canada |
| |
|
| Platform ID |
GPL8499 |
| Series (1) |
| GSE15889 |
Genome Variation in the Symbiotic Nitrogen-Fixing Bacterium Sinorhizobium meliloti |
|
