|
| Status |
Public on Apr 02, 2013 |
| Title |
25°C-4A, biological rep3 |
| Sample type |
RNA |
| |
|
| Source name |
Cells of Pseudomonas aeruginosa growth in PPGAS media at 25° C and harvested at O.D600 1.5
|
| Organism |
Pseudomonas aeruginosa |
| Characteristics |
strain: PAO1
growth temperature: 25° C
|
| Treatment protocol |
Samples were harvested at O.D600 of 1.5 and cells from 2.0 ml of each culture, was suspended in 0.5 ml of fresh PPGAS media and added to 1.0 ml of RNA Protect bacteria solution (Qiagen).
|
| Growth protocol |
Cells were grown in 15 ml of LB at 37 °C with shaking for 16 hours. Overnight precultures were diluted to an O.D600 of 0.05 in PPGAS media and grown at 25 °C and 37 °C, respectively.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was purified using the RNAeasy spin column RNeasy columns (Qiagen) according to the manufacturer’s instructions and residual DNA was eliminated by DNase treatment using RNase-free DNaseI (Thermo Scientific).
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Protocol-Technical Manual, 2001, Affymetrix).
|
| |
|
| Hybridization protocol |
Following fragmentation, 1 ug of cDNA were hybridized for 16 hr at 50°C on GeneChip P. aeruginosa Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
|
| Scan protocol |
GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
|
| Description |
PGAS_25_4A
Gene expression data from cells growth in PPGAS media at 25° C
|
| Data processing |
Data analyses from three biological replicates for each of the conditions tested were performed after normalizing and summarizing probe level measurements using Robust Multiarray Average (RMA). All microarray data analysis was performed using microarray software package Partek Genomic Suite 6.5. Only genes that fit stringent criteria (expression cutoff: 50–100% stringency; p-value ≤0.01 of one-way ANOVA data corrected by Benjamini Hochberg FDR; fold-change ≥1.4) were selected for further analysis.
|
| |
|
| Submission date |
Apr 01, 2013 |
| Last update date |
Apr 02, 2013 |
| Contact name |
Victoria Grosso |
| E-mail(s) |
mvgb28@yahoo.com
|
| Organization name |
Instituto de Investigaciones Biomédicas UNAM
|
| Department |
Biología Molecular y Biotecnología
|
| Street address |
Tercer circuito exterior C.U
|
| City |
México D.F |
| ZIP/Postal code |
04510 |
| Country |
Mexico |
| |
|
| Platform ID |
GPL84 |
| Series (1) |
| GSE45695 |
Regulation by growth temperature of Pseudomonas aeruginosa quorum-sensing depedent virulence factors production involves two RNA-thermometers. |
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