|
| Status |
Public on Sep 20, 2011 |
| Title |
Strain p11 isolated from in vitro biofilm rep. 2 |
| Sample type |
RNA |
| |
|
| Source name |
Strain p11 isolated from in vitro biofilm rep. 2
|
| Organism |
Pseudomonas aeruginosa |
| Characteristics |
strain: PBCLOp11
initial isolate source: burn wound isolate
infection model isolate source: in vitro biofilm
|
| Treatment protocol |
RNAprotect QIAGEN, human sample collected with sterile swab which was deepen in RNAprotect
|
| Growth protocol |
Burn wound - collection from wound and stabilization in RNAprotect (QIAGEN), Murine tumore - 5 mice with tumor per strain infected intravenously with P. aeruginosa, Tumors extracted after 24h homogenized with stabilization of the RNA, Plant - Lettuce leaves infected with P. aeruginosa, infection sites stabilized and RNA extracted after 5 days of incubations, Planktonic LB - early stationary phase - RNAprotect, Biofilm - 24h biofilm on plastic slide and 10% LB - RNAprotect
|
| Extracted molecule |
total RNA |
| Extraction protocol |
QIAGEN RNAmini, Ambion MicrobEnrich, Ambion MessageAMP
|
| Label |
biotin
|
| Label protocol |
Biotin incorporation during amplification
|
| |
|
| Hybridization protocol |
Standard affymetrix
|
| Scan protocol |
Standard affymetrix
|
| Description |
In vitro P. aeruginosa gene expression from biofilm
|
| Data processing |
Data analysis was performed using the R version 2.6.0 and Bioconductor version 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 |
Jul 19, 2010 |
| Last update date |
Sep 20, 2011 |
| Contact name |
Piotr Bielecki |
| E-mail(s) |
pbi@helmholtz-hzi.de
|
| 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) |
| GSE23007 |
In-Vivo Expression Profiling of Pseudomonas aeruginosa Infections Reveals Niche-Specific and Strain-Independent Transcriptional Programs |
|
