|
| Status |
Public on Dec 04, 2014 |
| Title |
Duck mock-infected control, biological rep2 |
| Sample type |
RNA |
| |
|
| Source name |
Primary lung cells derived from 6-week-old Pekin ducks, mock infection
|
| Organism |
Anas platyrhynchos |
| Characteristics |
age: 6 weeks
cell type: primary lung cells
treatment: mock infection
treatment duration: 24 hrs
|
| Treatment protocol |
Monolayers of primary cells in 6-well cell culture plates (Costar) were infected with LPAI and HPAI viruses at multiplicity of infection (MOI) of 1.0. Three wells of each cell type were used for each of the three viruses. Negative controls were performed in triplicate wells for each cell type without virus infection.
|
| Growth protocol |
Cells were grown in collagen-coated cell culture flasks (Costar) in DMEM and Ham’s F12 (1:1) supplemented with 2% chicken embryo extract (Biosera), 5% fetal calf serum, 1% insulin-transferrin selenium (Invitrogen) and antibiotics.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Twenty-four hours following infection, total RNA from each well was extracted using the RNeasy Mini - QIAshredder Kit (Qiagen) following the manufacturer’s instructions.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared with 100ng of total RNA using the GeneChip® 3′ IVT Express Kit (Affymetrix) following the manufacturer’s instructions.
|
| |
|
| Hybridization protocol |
12.5µg of labeled and fragmented aRNA were hybridized to a GeneChip® Chicken Genome Array (Affymetrix) for 16hrs at 45 °C.
|
| Scan protocol |
GeneChips were scanned using a GeneChip® Scanner 3000 with AGCC scan control software (Affymetrix).
|
| Description |
Duck_Control-mock infected_2
Gene expression data from mock-infected duck lung cells at 24h post-infection.
|
| Data processing |
Gene expression analysis was carried out using the GeneSpring GX10 expression analysis software (Agilent Technologies). Probe summarization was carried out by the Robust Multichip Averaging (RMA) summarization algorithm, followed by baseline transformation using baseline to median of all samples. Statistical analysis was carried out by analysis of variance (ANOVA) with a p value cut-off of 0.05 by asymptotic p-value computation algorithm with no multiple testing correction.
|
| |
|
| Submission date |
Nov 01, 2011 |
| Last update date |
Dec 04, 2014 |
| Contact name |
Suresh Varma Kuchipudi |
| E-mail(s) |
[email protected]
|
| Phone |
+44 (0) 115916653
|
| Organization name |
University of Nottingham
|
| Department |
School of Veterinary Medicine and Science
|
| Lab |
Infection and Immunity
|
| Street address |
College Road
|
| City |
Sutton Bonington |
| ZIP/Postal code |
LE12 5RD |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL3213 |
| Series (1) |
| GSE33389 |
Expression data from low- and high-pathogenicity avian influenza-infected chicken and duck cells |
|
