|
| Status |
Public on Jan 29, 2013 |
| Title |
PBS |
| Sample type |
RNA |
| |
|
| Source name |
Infected ferrets non-depleted of alveolar macrophages
|
| Organism |
Mustela putorius |
| Characteristics |
tissue: Lung RNA
|
| Treatment protocol |
Influenza virus infected and uninfected
|
| Growth protocol |
In-vivo (ferret's lung)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extraction using Trizol
|
| Label |
Cy3
|
| Label protocol |
Amplified and labeled cRNA was purified on cRNA Cleanup Module (Agilent Technology) according to the manufacturer’s protocol. Labeled cRNA target was quantified using ND-1000 spectrophotometer (NanoDrop Technologies, Inc., Wilmington, DE).
|
| |
|
| Hybridization protocol |
After checking labeling efficiency, fragmentation of cRNA was performed by adding 10X blocking agent and 25X fragmentation buffer and incubating at 60oC for 30 min. The fragmented cRNA was resuspended with 2X hybridization buffer and directly pipetted onto assembled Agilent’s Rat Oligo Microarray (44K). The arrays hybridized at 65oC for 17 hours using Agilent Hybridization oven (Agilent Technology, USA). The hybridized microarrays were washed as the manufacturer’s washing protocol (Agilent Technology, USA).
|
| Scan protocol |
The hybridized images were scanned using Agilent’s DNA microarray scanner and quantified with Feature Extraction Software (Agilent Technology, Palo Alto, CA).
|
| Description |
PBS_252119310614_1_1
|
| Data processing |
All data normalization and selection of fold-changed genes were performed using GeneSpringGX 7.3 (Agilent Technology, USA). The averages of normalized ratios were calculated by dividing the average of normalized signal channel intensity by the average of normalized control channel intensity. Functional annotation of genes was performed according to Gene OntologyTM Consortium (http://www.geneontology.org/index.shtml) by GeneSpringGX 7.3. Gene classification was based on searches done by BioCarta (http://www.biocarta.com/), GenMAPP (http://www.genmapp.org/), DAVID (http://david.abcc.ncifcrf.gov/), and Medline databases (http://www.ncbi.nlm.nih.gov/).
|
| |
|
| Submission date |
Jan 28, 2013 |
| Last update date |
Jan 29, 2013 |
| Contact name |
Heui Man Kim |
| E-mail(s) |
animal80@hanmail.net
|
| Fax |
82428216762
|
| URL |
http://www.cnuflulab.com/
|
| Organization name |
Chungnam national university
|
| Department |
College of Veterinary Medicine
|
| Lab |
Lab. of Influenza Research
|
| Street address |
99 Daehak ro
|
| City |
Deajeon |
| State/province |
Deajeon |
| ZIP/Postal code |
305-764 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL15379 |
| Series (1) |
| GSE43813 |
The Severe Pathogenicity of Infected Ferrets Depleted of Alveolar Macrophages with 2009 Pandemic H1N1 Influenza Virus |
|
