|
| Status |
Public on Aug 14, 2012 |
| Title |
IM003_Mu_mock_d1_1 |
| Sample type |
RNA |
| |
|
| Source name |
Lung, mock infection, day 1
|
| Organism |
Mus musculus |
| Characteristics |
strain: BALB/c
gender: female
age: 6-8 weeks
tissue: lung
treatment: mock infection
time of sample collection: day 1 post-inoculation
|
| Treatment protocol |
Six-to-eight-week-old female BALB/c mice were anesthetized and inoculated with either 50 μl of phosphate-buffered saline (PBS; Mock) or with 10^6 pfu of pandemic H1N1 influenza A/California/04/2009 virus in a 50 μl volume. Nine animals for the infection group were used for array analysis, three animals per time point. Eight animals for the mock group were used for array analysis, three animals for the day 1 and 3 time points and 2 animals for the day 5 time point.
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 Mouse Whole Genome Gene Expression Microarray (G4122F) slides.
|
| Scan protocol |
Dry slides were scanned on an Agilent Technologies Scanner (Model G2505C) using the XDR setting.
|
| Description |
251486830673_1_3
|
| 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 the Agi4x44PreProcess package.
|
| |
|
| Submission date |
Aug 13, 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 |
GPL7202 |
| Series (2) |
| GSE40091 |
Comparative transcriptomic analysis of acute host responses during 2009 pandemic H1N1 influenza infection in mouse, macaque, and swine (mouse dataset) |
| GSE40092 |
Comparative transcriptomic analysis of acute host responses during 2009 pandemic H1N1 influenza infection in mouse, macaque, and swine |
|
