|
| Status |
Public on Mar 31, 2013 |
| Title |
Lung-VN62-12h-S4 |
| Sample type |
RNA |
| |
|
| Source name |
wild-type C57BL/6J mice lung tissue
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6J
infection (influenza strain): VN62
time (hours): 12
|
| Treatment protocol |
Virus aliquots stored at -80C; quick thaw to RT and immediate dilution. Viruses diluted to 1x10^5 PFU/30ul (3.33x10^6 PFU/ml) in ice-cold 1x PBS in polystyrene tubes. Virus dilution maintained at 4C until use. Mice are all female C57BL/6J from Jackson Lab.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Mice were sacrificed by CO2 inhalation. Whole lungs (right side) removed and homogenized (with bead homogenizer) in 1 ml Trizol. Samples snap frozen in liquid nitrogen.
|
| Label |
Cy3
|
| Label protocol |
Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng total RNA using Agilent’s Low Input Quick Amp One-Color Labeling Kit according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and
|
| |
|
| Hybridization protocol |
600 ng of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions.
|
| Scan protocol |
Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using the Agilent G3-1-color scan setting for 8x60k arrays.
|
| Description |
Lung tissue after stimulation with either PR8, VN, X31 or Mock for 12 hours
|
| Data processing |
The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 028005_D_F_20101029).
|
| |
|
| Submission date |
Nov 14, 2012 |
| Last update date |
Mar 31, 2013 |
| Contact name |
Aderem Lab |
| E-mail(s) |
alan.diercks@seattlechildrens.org
|
| Organization name |
Seattle Children's Research Institute
|
| Lab |
Aderem Lab
|
| Street address |
307 Westlake Avenue North, Suite 500
|
| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98109 |
| Country |
USA |
| |
|
| Platform ID |
GPL10787 |
| Series (1) |
| GSE42285 |
Host response in the lung to influenza infection with PR8, VN or X31 strains at 12, 16 and 24 hours |
|
