|
| Status |
Public on Jul 10, 2012 |
| Title |
WT Tx vs. Mock 12hr 4 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
A549 mock treated, 12hr
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: A549
infection: mock
time: 12hr
|
| Growth protocol |
A549 cells were infected with human H1N1 influenza A/Texas/91 virus (Tx/91) or recombinant influenza Tx/91 NS1:1-126 virus. A549 cells were harvested at 12 and 24 hr post-infection. HTBE cells were harvested at 9.5 and 24 hrs post infection for microarray.
HTBE cells were homogenized in TRIzol reagent, and A549 cells were lysed in solution D (4 M guanidinium thiocyanate, 25 mM sodium citrate, 0.5 % sarcosyl, 0.1 M β-mercaptoethanol) and kept at -80 degrees C prior to RNA isolation.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Lysates were were phase-separated, and RNA was isolated from the aqueous phase using Qiagen RNeasy columns and the manufacturer’s recommended protocol (Qiagen Inc., Valencia, CA). RNA quality was assessed on an Agilent Bioanalyzer using the nanochip format, and only intact RNA was used for microarray analyses.
|
| Label |
Cy3
|
| Label protocol |
Cy3- and Cy5-labeled cRNA probes were generated by using an Agilent Low RNA Input Linear Amplification kit.
|
| |
|
| Channel 2 |
| Source name |
A549 Tx/91 treated, 12hr
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: A549
infection: influenza Tx/91
time: 12hr
|
| Growth protocol |
A549 cells were infected with human H1N1 influenza A/Texas/91 virus (Tx/91) or recombinant influenza Tx/91 NS1:1-126 virus. A549 cells were harvested at 12 and 24 hr post-infection. HTBE cells were harvested at 9.5 and 24 hrs post infection for microarray.
HTBE cells were homogenized in TRIzol reagent, and A549 cells were lysed in solution D (4 M guanidinium thiocyanate, 25 mM sodium citrate, 0.5 % sarcosyl, 0.1 M β-mercaptoethanol) and kept at -80 degrees C prior to RNA isolation.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Lysates were were phase-separated, and RNA was isolated from the aqueous phase using Qiagen RNeasy columns and the manufacturer’s recommended protocol (Qiagen Inc., Valencia, CA). RNA quality was assessed on an Agilent Bioanalyzer using the nanochip format, and only intact RNA was used for microarray analyses.
|
| Label |
Cy5
|
| Label protocol |
Cy3- and Cy5-labeled cRNA probes were generated by using an Agilent Low RNA Input Linear Amplification kit.
|
| |
|
| |
| Hybridization protocol |
Microarray slide hybridization was performed with Agilent human microarrays according to the manufacturer’s instructions. Each microarray experiment was done with four technical replicates by reverse dye hybridization for experimental and reference samples.
|
| Scan protocol |
Dry slides were scanned on an Agilent DNA microarray scanner (Model G2505B).
|
| Data processing |
Raw images were analyzed using the Agilent Feature Extraction software (version 8.1.1.1) and the GE2-v5_95_Feb07 extraction protocol.
|
| |
|
| Submission date |
Jul 09, 2012 |
| Last update date |
Jul 10, 2012 |
| Contact name |
Michael Katze |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Washington
|
| Department |
Microbiology
|
| Lab |
Michael G. Katze, Ph.D
|
| Street address |
Rosen Building 960 Republican St.
|
| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98109-4325 |
| Country |
USA |
| |
|
| Platform ID |
GPL4133 |
| Series (2) |
| GSE39200 |
The NS1 protein of influenza A virus suppresses interferon-regulated activation of antigen-presentation and immune-proteasome pathways |
| GSE39202 |
NS1 protein of influenza A virus and interferon |
|
