|
| Status |
Public on May 25, 2015 |
| Title |
P. aeruginosa PAO1, control |
| Sample type |
RNA |
| |
|
| Source name |
P. aeruginosa PAO1, control
|
| Organism |
Pseudomonas aeruginosa PAO1 |
| Characteristics |
agent: control
|
| Treatment protocol |
Sample 2 was incuabted with 1 mM ZnO nanoparticle at 37oC for 5 hrs with 250 rpm shaking
|
| Growth protocol |
P. aeruginosa was inoculated in 25 ml of LB medium in 250 ml shaker flasks with overnight cultures (1 : 100 dilution). Cells were cultured for 5 h with shaking at 250 rpm with and without ZnO nanoparticles (1 mM).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
DNA microarray analysis with one biological replicate was performed with an Affymetrix system. P. aeruginosa was inoculated in 25 ml of LB medium in 250 ml shaker flasks with overnight cultures (1 : 100 dilution). Cells were cultured for 5 h with shaking at 250 rpm with and without ZnO nanoparticles (1 mM). Before sample collection, RNase inhibitor (RNAlater, Ambion, TX, USA) was added, and the cells were immediately chilled with dry ice and 95% ethanol (to prevent RNA degradation) for 30 s before centrifugation at 16,000 g for 2 min. The cell pellets were immediately frozen with dry ice and stored at –80°C. Total RNA was isolated using a Qiagen RNeasy mini Kit (Valencia, CA, USA) with Qiagen RNase-free DNase I (Cat# 79254).
|
| Label |
biotin
|
| Label protocol |
Following affymetrix protocol. cDNA was synthesized first using Promega M-MLV Reverse transcriptase (cat# M1705). After removing RNA, DNA fragmentation was performed to obtain and 50-200 base cDNA fragments. The fragmented cDNA was labelled with Biotin-ddUTP using Enzo BioArray Terminal Labeling Kit (Affymetrix, P/N 900181).
|
| |
|
| Hybridization protocol |
Following affymetrix protocol. Prepared hybridization cocktail for Single Probe Array (49 Format) with total 200 ul volume including 1X hybrization buffer, 50 pM B2 Control Oligo, 0.1 mg/mL Herring Sperm DNA, 0.5 mg/mL BSA, and at least 1 ug fragmented and labelled cDNA. After loading of hybridization cocktail in Affymetrix E. coli Antisense Genome Array, the hybridization was performed at 45ºC, with 60 rpm for 16 hours. After hybridization, the probe array was washed and stained using Affymetrix Genechip Fluidics Station 450 and the software GenomeChipOperating Software (GCOS).
|
| Scan protocol |
Following affymetrix protocol. After washing and staining, the probe array was scanned using Affymetrix Genechip scanner GCS3000 7G system and the software GenomeChipOperating Software (GCOS).
|
| Description |
SAMPLE 1
Gene expression data of Pseudomonas aeruginosa PAO1 incubated for 5 hrs at 37oC with 250 rpm shaking
|
| Data processing |
MAS 5.0 Expression Analysis Default Setting
|
| |
|
| Submission date |
May 15, 2013 |
| Last update date |
May 25, 2015 |
| Contact name |
Jintae Lee |
| E-mail(s) |
jtlee@ynu.ac.kr
|
| Phone |
82-53-810-2533
|
| Organization name |
Yeungnam University
|
| Department |
Chemical engineering
|
| Lab |
Biotechnology
|
| Street address |
214-1 Daedong
|
| City |
Gyeongsan-Si |
| State/province |
Gyeongsangbuk-Do |
| ZIP/Postal code |
712-749 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL84 |
| Series (1) |
| GSE46947 |
Antivirulence activities of zinc ion and ZnO nanoparticle against Pseudomonas aeruginosa |
|
