|
| Status |
Public on Nov 04, 2010 |
| Title |
biofilm grown QS+ strain UUPA38, biological rep 1 |
| Sample type |
RNA |
| |
|
| Source name |
UUPA38 biofilm culture 1
|
| Organism |
Pseudomonas aeruginosa |
| Characteristics |
tissue: bacterial cells
strain: UUPA38
quorum sensing (qs) phenotype: QS+
culture: biofilm
|
| Growth protocol |
Biofilms were grown for 5 days in Luria Bertani broth at 22°C as 1 m flow-through tube cultures (bore=5 mm; flow rate=0.5 ml/min)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the RNeasy Mini Purification Kit (Qiagen) with lysozyme being applied at 1 mg/ml rather than the recommended 400 µg/ml. 10 mg of total RNA was used for cDNA synthesis.
|
| Label |
biotin
|
| Label protocol |
cDNA was labelled according to the standard Affymetrix protocol (Affymetrix GeneChip® Expression Analysis Technical Manual 701021 Rev. 5) using GeneChip® DNA Labeling Reagent (Affymetrix).
|
| |
|
| Hybridization protocol |
All labelled product was added to the hybridisation cocktail as required for a 100 Format (midi) array and hybridised to a GeneChip® P. aeruginosa Genome Array for 16 h at 50˚C. The array was washed and stained according to the pre-defined fluidics script on a GeneChip® Fluidics Station 450
|
| Scan protocol |
GeneChips were scanned using an Affymetrix GeneChip® Scanner 3000.
|
| Description |
Gene expression data from QS+ P. aeruginosa strain UUPA38 grown as biofilm.
|
| Data processing |
Data were normalised per-chip to the median and per-gene to the QS+ isolate in GeneSpring GX. Hierarchical clustering of genes present or marginal in all samples, using Spearman correlation as the similarity measure and Average Linkage as the clustering algorithm, showed clustering of the samples first by isolate, and then based on mode of growth. Principle components analysis was performed by Partek Pro 5.1. Genes consistently present or marginal were analysed by Student’s t-test to determine the significance of expression ratios.
|
| |
|
| Submission date |
Nov 03, 2010 |
| Last update date |
Nov 03, 2010 |
| Contact name |
Sally Helene Pattison |
| E-mail(s) |
s.pattison@qub.ac.uk
|
| Organization name |
Queen's University Belfast
|
| Department |
Centre for Infection & Immunity
|
| Street address |
MBC 97 Lisburn Road
|
| City |
Belfast |
| ZIP/Postal code |
BT9 7BL |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL84 |
| Series (2) |
| GSE25128 |
Gene expression data from Pseudomonas aeruginosa strains isolated from cystic fibrosis lung infections |
| GSE25130 |
Novel virulence factors in host-adapted Pseudomonas aeruginosa infection of the Cystic Fibrosis airways |
|
