|
| Status |
Public on Feb 13, 2012 |
| Title |
Sw_H1N1_2009_Mock_Day3_E5_4 |
| Sample type |
RNA |
| |
|
| Source name |
Lung
|
| Organism |
Sus scrofa |
| Characteristics |
viral strain: none - mock
dose: none
animal id: 4
date of viral origin: 2009
day of sample collection post-innoculation: Day3
tissue: lung
|
| Treatment protocol |
Tissue samples were prepared as TRIZol homogenates for subsequent RNA extraction (QIAGEN, RNeasy kit).
|
| Growth protocol |
In each experiment, 10 pigs were inoculated with noninfectious cell culture supernatant as controls. For the classical H1N1 SIV experiment, 10 4-week-old crossbred pigs were inoculated intratracheally with 10^6 50% tissue culture infective doses (TCID50)/pig of egg-derived IA30 virus. For the pH1N1 virus experiment, 10 4-week-old crossbred pigs were inoculated intratracheally with 10^6 TCID50/pig of either egg-derived CA/09 or Alb/09 virus. Five animals per group were euthanized at 3 and 5 days postinfection (dpi), respectively.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Global gene expression was measured by microarray in samples of lung lobes of animals that were euthanized and necropsied on days 3 and 5 post infection with A/California/04/2009 (n=5 per time point), A/swine/Alberta/25/2009 (n=5 per time point), or A/swine/Iowa/15/1930 (n=5 per time point), or mock infected (n=5 per time point) . All TRIzol lysates were processed simultaneously: they were phase-separated, and RNA was isolated from the aqueous phase (diluted 2 fold with RLT buffer) using Qiagen RNeasy Mini columns and the manufacturer’s recommended protocol (Qiagen Inc., Valencia, CA). RNA quality was assessed on an Agilent 2100 Bioanalyzer using the nanochip format, and only intact RNA was used for microarray analyses.
|
| Label |
Cy3
|
| Label protocol |
The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol with Low Input Quick Amp Labeling was followed for all processing steps, including Cy3-cDNA probe preparation, hybridization and array washing.
|
| |
|
| Hybridization protocol |
The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for all processing steps, including Cy3-cDNA probe preparation, hybridization and array washing.
|
| Scan protocol |
Dry slides were scanned on an Agilent DNA microarray scanner (Model G2505C).
|
| Description |
US93503719_252010910523_S01_GE1-v5_95_Feb07_1_3.txt
|
| 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.
Agilent Feature extractor software: 9.5.3.1
platform x86_64-redhat-linux-gnu
arch x86_64
os linux-gnu
system x86_64, linux-gnu
R version 2.12.2 (2011-02-25)
bioconductor packages: limma
Information on package 'limma'
Description:
Package: limma
Version: 3.6.9
Date: 2010/12/01version
For the creation of the normalized data matrix, the limma package was used. Background correction was performed (method="normexp", offset=1).
Data was quantile normalized between arrays with the quantile normalization method and then log2 transformed.
|
| |
|
| Submission date |
Feb 13, 2012 |
| Last update date |
Feb 14, 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) |
| GSE35738 |
2009 pandemic H1N1 virus causes disease and upregulation of genes related to inflammatory and immune response, cell death, and lipid metabolism in pigs |
| GSE40092 |
Comparative transcriptomic analysis of acute host responses during 2009 pandemic H1N1 influenza infection in mouse, macaque, and swine |
|
