|
| Status |
Public on Apr 21, 2009 |
| Title |
Pseudomonas aeruginosa (pMUM3) (2) |
| Sample type |
RNA |
| |
|
| Source name |
Pseudomonas aeruginosa (pMUM3) (2)
|
| Organism |
Pseudomonas aeruginosa |
| Characteristics |
strain: Pseudomonas aeruginosa PAO25 containing the plasmid pMUM3
|
| Growth protocol |
Grown in 300 mL Erlenmeyer flask with 30 mL LB and 25 µg/ml piperacillin at 37°C and 200 revolutions per min.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated by the hot phenol method using the Tri Reagent® LS (Molecular Research Center, Inc.). Contaminating DNA was eliminated by Dnase I (Amersham) treatment, and RNA was isolated by phenol-chloroform extraction and precipitation with 2.5 x volume 100% (vol/vol) ethanol and 0.1 x volume 3 M sodium acetate pH 4.8. An additional RNA purification step was performed using the RNeasy columns (Qiagen). RNA quantity was assessed by UV absorption at 260 nm in a ND-1000 Spectrophotometer (NanoDrop Technologies, USA). RNA quality was monitored by 1.5% (wt/vol) agarose gel electrophoresis containing 2,2 M formaldehyde as denaturing agent.
|
| Label |
Enzo BioArrayTM Terminal Labeling kit (Affymetrix)
|
| Label protocol |
Enzo BioArrayTM Terminal Labeling kit (Affymetrix)
|
| |
|
| Hybridization protocol |
Target hybridization, washing, staining and scanning were performed by the Affymetrix Core Facility using a GeneChip® hybridization oven, a Fluidics station and MICROARRAY SUITE software (Affymetrix)
|
| Scan protocol |
Target hybridization, washing, staining and scanning were performed by the Affymetrix Core Facility using a GeneChip® hybridization oven, a Fluidics station and MICROARRAY SUITE software (Affymetrix)
|
| Description |
Target hybridization, washing, staining and scanning were performed by the Affymetrix Core Facility using a GeneChip® hybridization oven, a Fluidics station and MICROARRAY SUITE software (Affymetrix)
|
| Data processing |
Target hybridization, washing, staining and scanning were performed by the Affymetrix Core Facility using a GeneChip® hybridization oven, a Fluidics station and MICROARRAY SUITE software (Affymetrix). Genes were considered differentially regulated if the relative change (n-fold) was >2.5 and the P value was <0.05.
|
| |
|
| Submission date |
Apr 16, 2009 |
| Last update date |
Apr 20, 2009 |
| Contact name |
Marian Llamas |
| E-mail(s) |
m.llamas@vumc.nl
|
| Organization name |
VU Medical Center
|
| Department |
Medical Microbiology
|
| Street address |
van der Boechorststraat 7
|
| City |
Amsterdam |
| ZIP/Postal code |
1081 BT |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL84 |
| Series (1) |
| GSE15697 |
A novel extracytoplasmic function (ECF) sigma factor regulates virulence in Pseudomonas aeruginosa |
|
