|
| Status |
Public on Mar 08, 2012 |
| Title |
VC617_Mock D1b |
| Sample type |
RNA |
| |
|
| Source name |
lung_Mock D1
|
| Organism |
Mus musculus |
| Characteristics |
strain: BALB/C
gender: female
sample collection time post infection: day 1
age: 6-8 weeks
infected with: phosphate-buffered saline (PBS; Mock)
condition group: Mock infected
|
| Treatment protocol |
Lung samples were stored in solution D (4 M guanidinium thiocyanate, 25 mM sodium citrate, 0.5% sarcosyl, 0.1 M β-mercaptoethanol) (5) at −80°C until processing.
|
| Growth protocol |
Six-to-eight-week-old female BALB/c mice were anesthetized and inoculated with 50 μl of phosphate-buffered saline (PBS; Mock) or with 106 pfu of virus in a 50 μl volume. Nine animals per condition group were used for array analysis, three animals per time point. There were seven condition groups: A/California/04/2009, MA1-A/California/04/2009, A/Mexico/4482/09, A/Brisbane/59/07, A/New Jersey/8/76, the reconstructed 1918 virus and time–matched mocks.
|
| 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 one Agilent 4X44K human HG (Design ID 014868) array.
|
| Scan protocol |
Dry slides were scanned on an Agilent DNA microarray scanner (Model G2505B) using the XDR setting.
|
| Description |
251486814145_1_4
|
| 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 (method=normexp, offset=1). Data was quantile normalized between arrays with the quantile normalization method and then log2 transformed using Agi4x44PreProcess and Bioconductor limma package.
|
| |
|
| Submission date |
Mar 07, 2012 |
| Last update date |
Mar 08, 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 |
GPL7202 |
| Series (1) |
| GSE36328 |
IM002, IM009 - Implication of inflammatory macrophages, nuclear receptors and interferon regulatory factors in increased virulence of pandemic 2009 H1N1 influenza A virus after host adaptation |
|
