|
| Status |
Public on Mar 30, 2012 |
| Title |
ampR mutant, uninduced, biological repl 1 |
| Sample type |
RNA |
| |
|
| Source name |
PAO∆ampR uninduced
|
| Organism |
Pseudomonas aeruginosa |
| Characteristics |
tissue: Whole cell
genotype: ampR mutant
age: Late log/ early stationary
agent: none
|
| Treatment protocol |
Mid log cells were exposed to sub-MIC concentrations of penicillin G. Untreated controls were maintained.
|
| Growth protocol |
P. aeruginosa PAO1 and PAO∆ampR were grown in LB medium in baffled flasks at 37 ˚C, 300 RPM
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from penicillin-treated and untreated cells using Rneasy Mini Kit (Qiagen) following manufacturer protocols.
|
| Label |
biotin
|
| Label protocol |
cDNA was prepared using SuperScript III reverse transcriptase, fragmented with RQ1 Dnase and biotin labeled.
|
| |
|
| Hybridization protocol |
Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on the Pseudomonas aeruginosa GeneChip (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
|
| Scan protocol |
GeneChips were scanned using the GeneArray 3000 7G Scanner, Affymetrix.
|
| Description |
Gene expression data from mutant cells unexposed to ß-lactams
|
| Data processing |
The data were analyzed with GeneSpring GX 10.0 Expression Analysis Software. Data normalization and sumarization was performed using GC-RMA. Other analysis parameters used were: expression cutoff of 50-100% stringency; p-value < 0.01 of one-way ANOVA data corrected by Benjamini Hochberg FDR; fold-change >2.0
|
| |
|
| Submission date |
Oct 24, 2011 |
| Last update date |
Mar 30, 2012 |
| Contact name |
Deepak Balasubramanian |
| E-mail(s) |
[email protected]
|
| Phone |
3053481261
|
| Organization name |
FLORIDA INTERNATIONAL UNIVERSITY
|
| Lab |
Mathee Lab
|
| Street address |
11200 SW 8th ST AHC1 #421
|
| City |
Miami |
| State/province |
Fl |
| ZIP/Postal code |
33199 |
| Country |
USA |
| |
|
| Platform ID |
GPL84 |
| Series (1) |
| GSE33188 |
Expression data from Pseudomonas aeruginosa PAO1 and its isogenic ampR mutant in the presence and absence of sub-MIC ß-lactam exposure. |
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