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Status |
Public on Dec 20, 2011 |
Title |
PAO1 delta PA1006 strain grown in NY+NO3 media, replicate 1 |
Sample type |
RNA |
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|
Source name |
Pseudomonas aeruginosa delta PA1006 mutant strain PAO1
|
Organism |
Pseudomonas aeruginosa |
Characteristics |
genotype/variation: delta PA1006/nbvF growth media: NY+NO3 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)
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|
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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+NO3 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).
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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 |
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