|
| Status |
Public on Mar 14, 2019 |
| Title |
hasset_PAO1_A |
| Sample type |
RNA |
| |
|
| Source name |
PAO1 WT grown under growth protocol
|
| Organism |
Pseudomonas aeruginosa PAO1 |
| Characteristics |
genotype/variation: wild type
|
| Treatment protocol |
Cells were treated with RNAprotect (Qiagen) and frozen at -80°C.
|
| Growth protocol |
transcriptional profiling experiments using wild-type PAO1, mucA22 and ∆mucA bacteria were grown for 24 hr under anaerobic conditions in LBN, pH 6.5, followed by treatment of each organism with 15 mM A-NO2- for 20 min.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were treated with RNAprotect (Qiagen) and total RNA was extracted using an RNeasy mini purification kit (Qiagen) per the manufacturer’s instructions. RNA quality and the presence of residual DNA were checked on an Agilent Bioanalyzer 2100 electrophoretic system pre- and post-DNase treatment.
|
| Label |
biotin
|
| Label protocol |
Ten micrograms of total RNA was used for cDNA synthesis, fragmentation, and labeling according to the Affymetrix GeneChip P. aeruginosa genome array expression analysis protocol (end labeled with biotin-ddUTP with use of the Enzo BioArray Terminal Labeling kit (Affymetrix))
|
| |
|
| Hybridization protocol |
Affymetrix GeneChip P. aeruginosa genome array expression analysis protocol.
|
| Scan protocol |
Affymetrix GeneChip P. aeruginosa genome array expression analysis protocol.
|
| Data processing |
Microarray data were generated using Affymetrix protocols. Probe set summarization (.CHP) files were generated using the Affymetrix Microarray Suite (MAS 5.0) algorithm. Background-corrected perfect match intensities were computed for each perfect match cell on every GeneChip and base-2 logarithm of each background-corrected perfect match intensity was obtained. These background-corrected and log-transformed perfect match intensities were normalized using the quantile normalization method. Tukey's median polish was used to obtain estimates that serve as the log-scale expression measures associated with the particular probe set. These data were imported into Transcriptome Analysis Console (Affymetrix version 3.0.0) Transcripts that were absent under both control and experimental conditions were eliminated from further consideration. Signal estimates for each transcript cluster for each condition was calculated using Tukey's Bi-weight Average Algorithm. Statistical significance of signals between the control and experimental conditions (P < 0.05) for individual transcripts was determined using the t test. Finally, the mean value of the signal log ratios from each comparison file was calculated. Only those genes that met the above criteria and had a mean signal log ratio of greater than or equal to 1 for up-regulated transcripts and less than or equal to 1 for down-regulated transcripts were kept in the final list of genes. Signal log ratio values were converted from log2 and expressed as fold changes.
|
| |
|
| Submission date |
Mar 13, 2019 |
| Last update date |
Mar 14, 2019 |
| Contact name |
Michael J Schurr |
| E-mail(s) |
michael.schurr@ucdenver.edu
|
| Phone |
3037244221
|
| Organization name |
University of Colorado School of Medicine
|
| Department |
Microbiology
|
| Street address |
12800 E 19th Ave
|
| City |
Aurora |
| State/province |
CO |
| ZIP/Postal code |
80045 |
| Country |
USA |
| |
|
| Platform ID |
GPL84 |
| Series (1) |
| GSE128220 |
The anti-sigma factor MucA of Pseudomonas aeruginosa: dramatic differences of mucA22 vs. DmucA mutants in anaerobic acidified nitrite sensitivity of planktonic and biofilm bacteria in vitro and during chronic murine lung infection |
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