|
| Status |
Public on Sep 12, 2012 |
| Title |
Sw_H1N1_2009_Mock_Day7_E5_13 |
| Sample type |
RNA |
| |
|
| Source name |
lung, mock infection, day 7
|
| Organism |
Sus scrofa |
| Characteristics |
breed: crossbred
tissue: lung
treatment: mock infection
time of sample collection: day 7 post-infection
|
| Treatment protocol |
Four-week-old crossbred pigs (Sus Scrofa) were inoculated intratracheally with either 10^6 TCID50/pig egg-derived 2009 pandemic influenza A/California/04/2009 virus (n = 5) or mock inoculated with non-infectious cell culture supernatant (control; n = 4). Animals were euthanized on day 7 post-infection and lung samples were used for microarray.
Lung samples were stored in solution D (4 M guanidinium thiocyanate, 25 mM sodium citrate, 0.5% sarcosyl, 0.1 M β-mercaptoethanol) at -80°C until processing.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Lung tissue was homogenized in solution D (4 M guanidinium thiocyanate, 25 mM sodium citrate, 0.5% sarcosyl, 0.1 M β-mercaptoethanol). RNA was isolated from lung lysates by precipitation using phenol-choloroform-isoamyl alcohol, then washed with isopropanol and resuspended in RNase-free water. The RNA concentration was measured using a Thermo Scientific Nanodrop 2000TM and the integrity of each RNA sample was determined using an Agilent 2100 Bioanalyzer.
|
| Label |
Cy3
|
| Label protocol |
The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for the Cy3-cDNA probe preparation.
|
| |
|
| Hybridization protocol |
The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for hybridization and array washing. Two hundred fifty ng of each RNA sample was hybridized to Agilent Porcine Gene Expression Microarray slides.
|
| Scan protocol |
Dry slides were scanned on an Agilent Technologies Scanner (Model G2505C) using the XDR setting.
|
| Description |
252010910522_1_1
|
| Data processing |
Raw images were analyzed using the Agilent Feature Extraction software (version 9.5.3.1) and the GE1-v5_95_Feb07 extraction protocol. All arrays were required to pass Agilent QC flags. Extracted raw data were background corrected using the norm-exp method and quantile normalized using Agi4x44PreProcess package.
|
| |
|
| Submission date |
Sep 12, 2012 |
| Last update date |
Sep 12, 2012 |
| Contact name |
Michael Katze |
| E-mail(s) |
data@viromics.washington.edu
|
| 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 |
GPL10162 |
| Series (2) |
| GSE40092 |
Comparative transcriptomic analysis of acute host responses during 2009 pandemic H1N1 influenza infection in mouse, macaque, and swine |
| GSE40847 |
Comparative transcriptomic analysis of acute host responses during 2009 pandemic H1N1 influenza infection in mouse, macaque, and swine (swine dataset) |
|
