|
| Status |
Public on Feb 22, 2013 |
| Title |
L control |
| Sample type |
RNA |
| |
|
| Source name |
Uninfected dog
|
| Organism |
Canis lupus familiaris |
| Characteristics |
tissue: lung
treatment: none
|
| Treatment protocol |
Influenza virus uninfected.
|
| Growth protocol |
In vivo (dog's lung).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extraction was performed using Trizol.
|
| Label |
Cy3
|
| Label protocol |
Amplified and labeled cRNA was purified using the cRNA Cleanup Module (Agilent Technology) according to the manufacturer's protocol. Labeled cRNA target was quantified using an 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 an assembled Agilent's Canine Oligo Microarray (44K). The arrays were hybridized at 65oC for 17 hours using an Agilent Hybridization oven (Agilent Technology, USA). The hybridized microarrays were washed as per 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).
|
| Data processing |
Agilent Feature Extraction Software (v 9.3.2.1) was used for background subtraction and LOWESS normalization. All data normalization and selection of fold-changed genes were performed using GeneSpring GX 7.3 (Agilent Technology, USA). The averages of the normalized ratios were calculated by dividing the average of the normalized signal channel intensity by the average of the normalized control channel intensity. Functional annotation of genes was performed according to the Gene OntologyTM Consortium (http://www.geneontology.org/index.shtml) by GeneSpring GX 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 |
Feb 21, 2013 |
| Last update date |
Feb 22, 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) |
| GSE44545 |
H3N2 canine influenza virus causes severe clinical signs in dogs with induction of genes related to inflammation and apoptosis |
|
