|
| Status |
Public on Feb 06, 2010 |
| Title |
J2315 vs. AMMD Replicate 2 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
Burkholderia ambifaria AMMD
|
| Organism |
Burkholderia ambifaria AMMD |
| Characteristics |
strain: Burkholderia ambifaria AMMD
|
| Growth protocol |
Strains were grown at 37°C in 10 ml Luria Bertani broth (Lennox formulation)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA from all strains was purified from 5 mL cultures grown in LB medium overnight at 37°C by the Wizard Genomic DNA Purification Kit (Promega, Madison, WI) according to the manufacturer’s instructions.
|
| Label |
Cy5
|
| Label protocol |
Two micrograms of genomic DNA from each strain was sonicated using a Heat Systems Ultrasonics W-225 20 kHz, 200 watt cup sonicator (Misonix, Farmingdale, NY) to generate sheared genomic DNAs from 0.5 to 5 kb. For each sample, 300 ug of sheared DNA was labeled using the methods described in (Wick et al. 2005). Equal amounts of tester and reference (J2315) samples with similar specific activities were mixed in 4 uL 10 mM EDTA pH8.0 and heated to 95C for 5 min.
|
| |
|
| Channel 2 |
| Source name |
Burkholderia cenocepacia J2315
|
| Organism |
Burkholderia cenocepacia J2315 |
| Characteristics |
strain: Burkholderia cenocepacia J2315
|
| Growth protocol |
Strains were grown at 37°C in 10 ml Luria Bertani broth (Lennox formulation)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA from all strains was purified from 5 mL cultures grown in LB medium overnight at 37°C by the Wizard Genomic DNA Purification Kit (Promega, Madison, WI) according to the manufacturer’s instructions.
|
| Label |
Cy3
|
| Label protocol |
Two micrograms of genomic DNA from each strain was sonicated using a Heat Systems Ultrasonics W-225 20 kHz, 200 watt cup sonicator (Misonix, Farmingdale, NY) to generate sheared genomic DNAs from 0.5 to 5 kb. For each sample, 300 ug of sheared DNA was labeled using the methods described in (Wick et al. 2005). Equal amounts of tester and reference (J2315) samples with similar specific activities were mixed in 4 uL 10 mM EDTA pH8.0 and heated to 95C for 5 min.
|
| |
|
| |
| Hybridization protocol |
Samples were mixed with 45 uL of SlideHyb buffer #1 (Ambion, Austin, TX) by pipetting. Hybridization mixes, loading procedures, and slide washing was performed according to Agilent’s recommended protocols (Agilent Technologies 2007) with a 16 h hybridization time at 65C with agitation and the optional Stabilization and Drying Solution final wash.
|
| Scan protocol |
Microarrays were scanned using an Axon GenePix 4000B scanner (Molecular Devices, Sunnyvale, CA) and probe intensities extracted using GenePix Pro 5.0 software.
|
| Description |
Biological replicate 2 of 2.
|
| Data processing |
The median background signal was subtracted from the mean probe signal and the ratio of background-subtracted signals of a tester to the reference strain were calculated for each probe and transformed to a logarithm base 10 ratio.
|
| |
|
| Submission date |
Jan 29, 2010 |
| Last update date |
Feb 05, 2010 |
| Contact name |
Deborah R. Yoder-Himes |
| Organization name |
Harvard Medical School
|
| Department |
Microbiology and Molecular Genetics
|
| Lab |
Lory Lab
|
| Street address |
77 Louis Pasteur Ave, 1038 NRB
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL9990 |
| Series (1) |
| GSE20096 |
Strains of increasing genetic divergence to the reference strain |
|
