|
| Status |
Public on Jul 21, 2022 |
| Title |
H6N1_6dpc_Mock_F_564_NP |
| Sample type |
RNA |
| |
|
| Source name |
6_H6N1_Mock
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Lung
virus strain: H6N1
day p.i.: 6
vaccination status: not vaccinated
|
| Treatment protocol |
Lung tissue collected from mice and stored in RNAlater according to manufacturer's instructions.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from lung tissue using RNAeasy (Qiagen) according to manufacturer's instructions. RNA quality was assessed using Agilent Bioanalyzer.
|
| Label |
Cy3
|
| Label protocol |
Cyanine-3 (Cy3) labeled cRNA was prepared from 0.3 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.
|
| |
|
| Hybridization protocol |
1.5 ug 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 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.
|
| Scan protocol |
Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).
|
| Description |
Gene expression profiling of lung tissue from influenza infected mice
|
| Data processing |
The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
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| |
|
| Submission date |
Jun 10, 2022 |
| Last update date |
Jul 21, 2022 |
| Contact name |
kathie walters |
| E-mail(s) |
kwalters@systemsbiology.org
|
| Organization name |
Institute for Systems Biology
|
| Street address |
401 Terry Ave N
|
| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98109 |
| Country |
USA |
| |
|
| Platform ID |
GPL7202 |
| Series (2) |
| GSE205839 |
An inactivated multivalent influenza A virus vaccine is broadly protective in mice and ferrets [mouse] |
| GSE205841 |
An inactivated multivalent influenza A virus vaccine is broadly protective in mice and ferrets |
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