|
| Status |
Public on Jun 01, 2011 |
| Title |
PYO Treated - repeat 1 - mAdbID:103983 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Untreated
|
| Organism |
Homo sapiens |
| Characteristics |
agent: Untreated
cell line: H292
cell type: epithelial
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol Extraction Protocol
Other: Total RNA was isolated using Trizol (Invitrogen) and an additional clean-up step was introduced using Qiagen "RNeasy mini-kit" RNA isolation kit.
|
| Label |
cy3
|
| Label protocol |
Cy3 Direct Labeling Protocol
Other: Total RNA (40 ug) was reverse transcribed to cDNA using oligo dT primers and SuperScript II RT. Double-stranded cDNA was synthesized using DNA polymerase with cy3-labeled dUTP with for direct dye incorporation. Clean-up was done with Vivaspin (Qiagen) column, washed four times, resuspended in RNase-free water.
|
| |
|
| Channel 2 |
| Source name |
PYO Treated
|
| Organism |
Homo sapiens |
| Characteristics |
agent: PYO Treated
cell line: H292
cell type: epithelial
|
| Treatment protocol |
Treatment type: compound
Agent: pyocyanin
Treatment dose: 8 uM
Treatment time: 48 hours
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol Extraction Protocol
Other: Total RNA was isolated using Trizol (Invitrogen) and an additional clean-up step was introduced using Qiagen "RNeasy mini-kit" RNA isolation kit.
|
| Label |
cy5
|
| Label protocol |
Cy5 Direct Labeling Protocol
Other: Total RNA (40 ug) was reverse transcribed to cDNA using oligo dT primers and SuperScript II RT. Double-stranded cDNA was synthesized using DNA polymerase with cy5-labeled dUTP with for direct dye incorporation. Clean-up was done with Vivaspin (Qiagen) column, washed four times, resuspended in RNase-free water.
|
| |
|
| |
| Hybridization protocol |
Agilent Hybridization Protocol
Other: Labeled RNA were hybridized to the microarrays using the TECAN HS Pro 4800 hybridization station with Agilent 2x Gene expression hybridization HI-RPM buffer and 10x Blocking Reagent at 65°C for 17 hours, and washed with Agilent Gene Expression Wash Buffer 1 at room temperature and Gene Expression Wash Buffer 2 at 37°C. Automation program “Agilent GE Protocol HPR“ included final drying step with nitrogen gas for 3 minutes.
|
| Scan protocol |
Agilent Scanning Protocol
Other: The slides were imaged using an Agilent high-resolution DNA microarray scanner G2505C at 5 um resolution and 100/10% PMT XDR. Agilent Feature Extraction software, protocol "GE2 105 Dec08", was used for image analysis.
|
| Description |
mAdb experiment ID: 103983
|
| Data processing |
JMP Genomics Data Processing
Calculation Method: Using MedianSignal column from Feature Extraction output, lowess normalization was used followed by re-centering all samples by subtracting the sample log2 median from each log2 expression measure. Normalized values were subjected to mixed-effects ANOVA with treatment as the fixed effect, array_id as the random effect.
|
| |
|
| Submission date |
Jun 17, 2010 |
| Last update date |
Jun 01, 2011 |
| Contact name |
Balazs Rada |
| E-mail(s) |
radab@mail.nih.gov
|
| Phone |
301 4356534
|
| Fax |
301 4801731
|
| Organization name |
NIH
|
| Department |
NIAID
|
| Lab |
Lab of Host Defenses
|
| Street address |
12441 Parklawn Drive
|
| City |
Rockville |
| State/province |
MD |
| ZIP/Postal code |
20852 |
| Country |
USA |
| |
|
| Platform ID |
GPL4133 |
| Series (1) |
| GSE22430 |
Inflammatory activation of airway epithelial cells by pyocyanin |
|
