|
| Status |
Public on Dec 20, 2011 |
| Title |
PAO1 delta PA1006 strain grown in NY media, replicate 2 |
| Sample type |
RNA |
| |
|
| Source name |
Pseudomonas aeruginosa delta PA1006 mutant strain PAO1
|
| Organism |
Pseudomonas aeruginosa |
| Characteristics |
genotype/variation: delta PA1006/nbvF
growth media: NY media
|
| Treatment protocol |
in parallel samples, 100mM KNO3 was added to the growth media
|
| Growth protocol |
growth was done aerobically shaking at 250rpm at 37 degrees Celcius in NY media supplemented with yeast extract until early stationary phase (OD600 ~1.2 )
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Tri-reagent (ambion was used to extract RNA; Residual DNA was removed with amplification grade DNAse I (Invitrogen) and RNA was concentrated using a MinElute kit (Qiagen). RNA integrity was assessed using a Bioanalyzer (Agilent Technologies, Foster, City, CA). cDNA synthesis, labeling, fragmentation, hybridization, and chip scanning was performed at the University of Rochester Core Facility.
|
| Label |
biotin
|
| Label protocol |
End-labeling of cDNA fragmented with Dnase I (Amersham) was done with Biotin-ddUTP and the Enzo BioArray terminal labeling kit (Affymetrix)
|
| |
|
| Hybridization protocol |
Hybridization was performed by using an Affymetrix Gen Chip System workstation equiped with Microarray Suite software (version 5.0), and a hybridization oven and fluidics workstation
|
| Scan protocol |
GeneChips were scanned using the Hewlett-Packard GeneArray Scanner.
|
| Description |
Gene expression data from cultures grown aerobically in NY media
|
| Data processing |
Transcript was detected using MAS software (version 5.0; Affymetrix) using default parameters. Pairwise comparisons were performed with Data Mining Tools (version 3.0; Affymetrix).
|
| |
|
| Submission date |
Apr 19, 2011 |
| Last update date |
Dec 20, 2011 |
| Contact name |
Barbara H. Iglewski |
| E-mail(s) |
Barbara_Iglewski@URMC.Rochester.edu
|
| Phone |
585-275-3402
|
| Organization name |
University of Rochester
|
| Department |
Microbiology and Immunology
|
| Lab |
Iglewski Lab
|
| Street address |
601 Elmwood Ave
|
| City |
Rochester |
| State/province |
NY |
| ZIP/Postal code |
14642 |
| Country |
USA |
| |
|
| Platform ID |
GPL84 |
| Series (1) |
| GSE28719 |
Gene expression of Pseudomonas aeruginosa (Pae) delta PA1006/nbvF mutant in the absence and presence of nitrate |
|
