|
| Status |
Public on Jun 13, 2012 |
| Title |
MPAO1 untreated rep.2 |
| Sample type |
RNA |
| |
|
| Source name |
MPAO1 untreated
|
| Organism |
Pseudomonas aeruginosa |
| Characteristics |
isolate: labratory strain MPAO1
compound: none
|
| Biomaterial provider |
Strain MPAO1 from UW Genom Sciences, Manoil Lab
|
| Treatment protocol |
Cultures of MPAO1 were collected on RNAprotect reagent, centrifuged and frozen until RNA extraction.
|
| Growth protocol |
Pseudomonas aeruginosa strains MPAO1 was grown overnight in ABT minimal medium supplemented with 0.5% casamino acids and inoculated 1% (v/v) in 200 mL of the same media and incubated at 37°C with shaking (250 rpm). When the culture reached middle exponential phase at an optical density of 0.5 at 600 nm (OD600), it was split into halves. One half was treated with 125 μM of Protoanemonin and the second served as a control. Cultures were harvested for proteomic and transcriptomic analysis (RNAprotect reagent, Qiagen) at the late exponential/early stationary phase at OD600 = 2.0 as described below. The experiment was performed in triplicate.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
QIAGEN RNAmini, Ambion MessageAMP. The total RNA from triplicates of each condition (biological replicates) were pooled together. Replicates of the microarray represent the technical replicates.
|
| Label |
biotin
|
| Label protocol |
Biotin incorporation during amplification
|
| |
|
| Hybridization protocol |
Standard affymetrix
|
| Scan protocol |
Standard affymetrix
|
| Description |
P. Aeruginosa gene expression from planctonic culture
|
| Data processing |
R version 2.6.0, Bioconductor 2.1. The quality of all chips was assessed by fitting a linear model to the probe level data using the function “fitPLM” from the “affyPLM” package. Subsequently, the distribution (boxplots) of RLE (Relative Log Expression) and NUSE (Normalised Unscaled Standard Errors) was manually analysed.
|
| |
|
| Submission date |
Mar 04, 2011 |
| Last update date |
Jun 13, 2012 |
| Contact name |
Piotr Bielecki |
| E-mail(s) |
[email protected]
|
| Phone |
+4953161813050
|
| Organization name |
Helmholtz Centre for Infection Research
|
| Department |
Cell Biology
|
| Lab |
Chronic Pseudomonas Infections
|
| Street address |
Inhoffenstr 7
|
| City |
Braunschweig |
| ZIP/Postal code |
38124 |
| Country |
Germany |
| |
|
| Platform ID |
GPL84 |
| Series (1) |
| GSE27674 |
Protoanemonin: A new natural quorum sensing inhibitor that selectively activates iron starvation response |
|
