|
| Status |
Public on Feb 12, 2014 |
| Title |
logarithmic A, biological rep2 |
| Sample type |
RNA |
| |
|
| Source name |
Pseudomonas aeruginosa parA mutant in logarithmic phase of growth
|
| Organism |
Pseudomonas aeruginosa |
| Characteristics |
strain/background: PAO1161
genotype: parA disruption mutant
growth phase: logarithmic
|
| Growth protocol |
Cells of P. aeruginosa PAO1161 derivative strains were taken from a deep-frozen stock, spread on L-agar plates and grown overnight at 37 degrees Cent. Bacteria from single colonies were then used to inoculate L broth (DifcoTM L Broth, Lennox, BD) liquid cultures and grown overnight with shaking at 37 degrees Cent. Three independent overnight cultures for each strain were diluted 1:100 into fresh L broth and grown with shaking at 37oC. Samples from the cultures were taken at regular intervals to measure the optical density at 600 nm (OD600) (UV-1800 Shimadzu Spectrophotometer) and to determine the c.f.u. ml-1. Aliquots of 2 ml from exponential phase cultures (OD600 0.5; c.f.u. ml-1 1 x 10^9 cells) were subjected to RNA extraction.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Three independent biological replicates of total RNA were isolated from each strain using a RNeasy mini-kit with on-column DNase digestion (Qiagen) according to the manufacturer's instructions followed by DNase digestion using TURBO DNase kit (Ambion) to eliminate DNA contamination.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cDNAs were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, (Affymetrix).
|
| |
|
| Hybridization protocol |
Following fragmentation, 10 ug of cDNA were hybridized for 16 hr at 45 degrees Cent. on GeneChip P. aeruginosa Genome Array in the Affymetrix GeneChip Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
|
| Scan protocol |
GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.
|
| Description |
PAO1161 Log A2
Gene expression data from logarithmic phase of growth of parA mutant.
|
| Data processing |
The microarray gene expression data was analyzed using Partek Genomic Suite 6.6 beta software (Partek Inc., Louis, MO). Raw data (.CEL files) were imported and processed, using GeneChip Robust Multiarray Averaging (GC RMA) background correction, quantile normalization, log2 transformation and median polish summarization.
|
| |
|
| Submission date |
May 16, 2013 |
| Last update date |
Feb 13, 2014 |
| Contact name |
Aneta Agnieszka Bartosik |
| E-mail(s) |
[email protected]
|
| Phone |
+48 22 5921215
|
| Organization name |
Polish Academy of Sciences
|
| Department |
Institute of Biochemistry and Biophysics
|
| Lab |
Depertment of Microbial Biochemistry
|
| Street address |
Pawinskiego 5A
|
| City |
Warsaw |
| ZIP/Postal code |
02-106 |
| Country |
Poland |
| |
|
| Platform ID |
GPL84 |
| Series (1) |
| GSE47031 |
Transcriptional profiling of Pseudomonas aeruginosa PAO1161 strain and its parA and parB mutants |
|
