|
| Status |
Public on Nov 14, 2012 |
| Title |
Strain p11 isolated from burn wound rep2 |
| Sample type |
RNA |
| |
|
| Source name |
Strain p11 isolated from burn wound rep. 2
|
| Organism |
Pseudomonas aeruginosa |
| Characteristics |
strain(s): PBCLOp11
initial p. aeruginosa isolate source: burn wound
rna extracted from: burn wound
|
| Treatment protocol |
RNAprotect QIAGEN, burn wound sample collected with sterile swab which was deepen in RNAprotect, CF mucuse sample mixed with RNAprotect
|
| Growth protocol |
Burn wound and CF sputum - collection and stabilization in RNAprotect (QIAGEN), Murine tumore - 3 mice with tumor per strain infected intravenously with P. aeruginosa, Tumors extracted after 24h homogenized with stabilization of the RNA, Planktonic LB - early stationary phase - 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 |
Ex vivo P. aeruginosa gene expression from burn wound
p11 burn 2
GBF0931 p11_clinical_b.CEL
Re-analysis of Sample GSM567679
|
| 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 |
Dec 09, 2010 |
| Last update date |
Nov 15, 2012 |
| 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) |
| GSE25945 |
Ex vivo transcriptional profiling reveals a common set of genes important for the adaptation of Pseudomonas aeruginosa to chronically infected host sites |
|
| Relations |
| Reanalysis of |
GSM567679 |
