|
| Status |
Public on Aug 04, 2006 |
| Title |
PA_WT - 0 Min - Replicate 2 |
| Sample type |
RNA |
| |
|
| Source name |
P. aeruginosa PAO1, 0 min post ciprofloxacin addition
|
| Organism |
Pseudomonas aeruginosa |
| Characteristics |
P. aeruginosa strain PAO1
|
| Treatment protocol |
Grow to mid-log in luria broth, treat with 1 ug/ml ciprofloxacin (~8x MIC). Take samples at 0, 30, 120 minutes post drug addition
|
| Growth protocol |
Luria broth at 37 C with shaking
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Qiagen RNeasy mini kit with RNAprotect reagent and on-column DNAse digestion
|
| Label |
biotin
|
| Label protocol |
standard Affymetrix Prokaryotic Target Preparation protocol as described at the Affymetrix website
|
| |
|
| Hybridization protocol |
standard Affymetrix Prokaryotic Target Preparation protocol as described at the Affymetrix website
|
| Scan protocol |
standard Affymetrix Prokaryotic Target Preparation protocol as described at the Affymetrix website
Chips were scanned using the Affymetrix ScanArray 3000 using default settings and a target intensity of 250 for scaling
|
| Description |
Present (P) and Absent (A) calls were determined with the Affymetrix algorithm (GCOS, Affymetrix, Santa Clara, CA). All marginal (M) calls were treated as absent (A). Probesets were considered present for a given condition if they had been assigned a present call in at least two of the three replicate samples for that condition.
|
| Data processing |
Present (P) and Absent (A) calls were determined with the Affymetrix algorithm (GCOS, Affymetrix, Santa Clara, CA). All marginal (M) calls were treated as absent (A). Probesets were considered present for a given condition if they had been assigned a present call in at least two of the three replicate samples for that condition.
|
| |
|
| Submission date |
Aug 02, 2006 |
| Last update date |
Aug 03, 2006 |
| Contact name |
Floyd Romesberg |
| E-mail(s) |
floyd@scripps.edu
|
| Phone |
8587847290
|
| Fax |
8587847472
|
| URL |
http://www.scripps.edu/chem/romesberg
|
| Organization name |
The Scripps Research Institute
|
| Department |
Chemistry
|
| Street address |
10550 N. Torrey Pines Road
|
| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92037 |
| Country |
USA |
| |
|
| Platform ID |
GPL84 |
| Series (1) |
| GSE5443 |
Defining the Pseudomonas aeruginosa SOS Response and its Role in the Global Response to the Antibiotic Ciprofloxacin |
|
