|
| Status |
Public on Sep 02, 2011 |
| Title |
ISP794_exponential_rep3 |
| Sample type |
RNA |
| |
|
| Source name |
wild type exponential phase cells replicate 3
|
| Organism |
Staphylococcus aureus |
| Characteristics |
strain: ISP794 (wild type)
cell phase: exponential
replicate: 3
|
| Biomaterial provider |
Quechi Truong-Bolduc
|
| Treatment protocol |
The experimental variable, or treatment, was the presence vs. absence of a functional norG gene. ISP794 contains a wild type copy of the norG gene, whereas QTII is an isogenic strain harboring a cat^R cassette
|
| Growth protocol |
S. aureus strains were grown to mid-exponential phase (Optical Density of 0.5) in BHI at 37oC on an orbital shaker (250 rpm); flask to volume ratio of 5:1
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Approximately 1 x 10^9 colony forming units of cell suspenseions were removed from culture flask and added to an equal vol (10 ml) of acetone:ethanol (1:1). Cells were pelleted by centrifugation at 1600 x g, the pellet was washed twice in TE buffer (10 mM Tris, 1 mM EDTA, pH 7.6) and resuspended in a final vol of 750 ul TE buffer. The cell suspension was mechanically disrupted in a Savant FastPrep 120 instrument. Total bacterial RNA was purified using Qiagen RNeasy mini-columns following the manufacturer's recommendations for prokaryotic RNA purification.
|
| Label |
biotin
|
| Label protocol |
10 micrograms of total bacterial RNA from each sample was biotinylated following Affymetrix recommendations for labeling prokaryotic RNA.
|
| |
|
| Hybridization protocol |
1.5 micrograms of biotinylated cDNA was hybridized for 16 hr at 45oC in Affymetrix hybridization oven. GeneChips were washed and stained in Affymetrix fluidics station 400.
|
| Scan protocol |
GeneChips were scanned in an Affymetrix GeneChip scanner 7N
|
| Data processing |
The data were analyzed using Affymetrix microarray suite 5.0 using default settings and global scaling as normalization method.
|
| |
|
| Submission date |
Aug 31, 2011 |
| Last update date |
Sep 02, 2011 |
| Contact name |
Paul Dunman |
| E-mail(s) |
[email protected]
|
| Phone |
585-276-5700
|
| Organization name |
University of Rochester
|
| Department |
Microbiology and Immunology
|
| Street address |
601 Elmwood Avenue
|
| City |
Rochester |
| State/province |
NY |
| ZIP/Postal code |
14642 |
| Country |
USA |
| |
|
| Platform ID |
GPL1339 |
| Series (1) |
| GSE31769 |
S. aureus expression properties of exponential ISP794 and isogenic norG mutant cells |
|
