|
| Status |
Public on Apr 10, 2012 |
| Title |
hour 0 post infection, 6 |
| Sample type |
RNA |
| |
|
| Source name |
Total RNA from infected A549 cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: A549 cells
infection: H1N1 infection
time [post-infection]: hour 0
|
| Treatment protocol |
A549 cells were infected with the H1N1 virus at a multiplicity of infection (MOI) of 0.1. Infection with S-OIV 2009 H1N1 was performed in the presence of 1 μg/ml TPCK-trypsin. Cell supernatant and RNA were collected at 0, 4, 8, 24, 48, and 72 hours post-infection (hpi). The 0-hour time-point corresponds to samples collected immediately after the 1-hour virus incubation with additional time-points numbered with regard to the end of viral incubation. Mock-infected A549 cells were propagated for each experiment with samples collected at the 72-hour time-point.
|
| Growth protocol |
All experiments with live influenza virus were performed at the National Center for Foreign Animal Diseases under biosafety level 3 (BSL3+) conditions. A/Mexico/InDRE4487/2009 (H1N1) stocks were propagated on MDCK (Madin Darby canine kidney) cells.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using the miRvana isolation kit (Ambion) following the instructions of the supplier.
|
| Label |
biotin
|
| Label protocol |
An input of 200 ng of total RNA was used to generate biotin-labeled cRNA following the Illumina TotalPrep RNA Amplification Kit (Ambion, Inc.)
|
| |
|
| Hybridization protocol |
Samples were hybridized on Illumina HumanHT-12 v3 BeadChips following the Illumina Whole-Genome Gene Expression Direct Hybridization Assay Guide (11286331).
|
| Scan protocol |
BeadChips were imaged and quantified with the Illumina iScan scanner.
|
| Description |
Sample name: h0.6
|
| Data processing |
Illumina GenomeStudio v2010.2 was used for data processing, which included averaging signal intensities for each unique Beadtype. GeneSpring 7.3.1 (Agilent Technologies) was used to median-normalize data to the 25th percentile. Analysis of the normalized data was carried out using R. The microarray profiling was performed at the Vancouver Prostate Centre Laboratory for Advanced Genome Analysis.
|
| |
|
| Submission date |
Mar 16, 2012 |
| Last update date |
Apr 10, 2012 |
| Contact name |
Victoria Svinti |
| Organization name |
University of British Columbia
|
| Street address |
2350 Health Sciences Mall
|
| City |
Vancouver |
| ZIP/Postal code |
V6T 1Z3 |
| Country |
Canada |
| |
|
| Platform ID |
GPL6947 |
| Series (2) |
| GSE36553 |
mRNA profiling during infection with H1N1 influenza A virus (A/Mexico/InDRE4487/H1N1/2009) |
| GSE36555 |
Host-influenza A virus(infA) interactions |
|
