|
| Status |
Public on Jul 03, 2010 |
| Title |
PAKH2O_1 |
| Sample type |
RNA |
| |
|
| Source name |
P. aeruginosa PAK from sterile water fed to mice
|
| Organism |
Pseudomonas aeruginosa |
| Characteristics |
strain: PAK
sample type: Drinking water
|
| Treatment protocol |
6-8 wk old C3H/HeN mice were given antibiotic water (streptomycin, penicillin G for 4 days), then given P. aeruginosa strain PAK in sterile water with pencillin for 5 days. Animals were euthanized and cecal contents (flushates) were recovered and immediately immersed in liquid nitrogen.
|
| Growth protocol |
Sterile water with 1500 units penicillin G/mL and P. aeruginosa strain PAK (107 cfu/mL) was stored in a sterile flask at RT for 24 hours.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Hot acid phenol/chloroform (Ambion) extraction protocol was utilized, followed by RQ1 Dnase (Promega) treatment and RNeasy cleanup protocol (Qiagen)
|
| Label |
biotin
|
| Label protocol |
12 ug of purified total RNA from cecal flushates or drinking water was converted to cDNA with Superscript II Reverse Transcriptase (Invitrogen) and a semi-random decamer, (NS)5 (Invitrogen). cDNA was partially digested with Dnase I and end labeled with ddUTP-biotin (Enzo Life Sciences)
|
| |
|
| Hybridization protocol |
4-7 ug of fragmented cDNA were hybridized for 15 hours at 50C on a GeneChip P. aeruginosa Genome Array. Genome arrays were washed and stained in the Affymetrix Fluidics Station.
|
| Scan protocol |
P. aeruginosa Genome Arrays were scanned using the Affymetrix GeneChip Scanner 3000
|
| Description |
Gene expression data from P. aeruginosa suspended in sterile water fed to adult C3H/HeN mice
|
| Data processing |
Intrachip normalizations were performed with Affymetrix Microarray Suite 5.0 software. Statistical analysis and experimental comparisons were made with GeneSpring version 4.2.1 (Agilent Technologies).
|
| |
|
| Submission date |
Jul 01, 2010 |
| Last update date |
Jul 02, 2010 |
| Contact name |
Andrew Koh |
| E-mail(s) |
andrew.koh@utsouthwestern.edu
|
| Fax |
214 648-4574
|
| Organization name |
University of Texas Southwestern Medical Center
|
| Department |
Pediatrics
|
| Lab |
Koh Lab
|
| Street address |
5323 Harry Hines Boulevard
|
| City |
Dallas |
| State/province |
TX |
| ZIP/Postal code |
75390-9063 |
| Country |
USA |
| |
|
| Platform ID |
GPL84 |
| Series (1) |
| GSE22665 |
Expression data from P. aeruginosa colonizing the Murine GI Tract |
|
