|
| Status |
Public on Mar 31, 2010 |
| Title |
OFTu + OV-IA82Δ024 at 4 hpi |
| Sample type |
RNA |
| |
|
| Source name |
Primary ovine fetal turbinate cells infected with ORFV strain OV-IA82Δ024 at 4hpi
|
| Organism |
Ovis aries |
| Characteristics |
tissue: primary ovine fetal turbinate cells
passage number: 10
time of culture before infection: 16 h
time post-infection: 4 h
|
| Treatment protocol |
OFTu cells were cultured in 35 mm dishes (7 X 10^5 cells/dish) for 16 hours and inoculated with 10 m.o.i of the Wild type virus (OV-IA82) or deletion mutant virus (OV-IA82Δ024). Cells were harvested and total RNA was extracted at 2 and 4 hours post-infection.
|
| Growth protocol |
OFTu cells were cultured in MEM supplemented with 10% of fetal bovine serum, 2 mM L-Glutamine, 50µg/mL of gentamicin, 100U/mL of Penicilin and 100µg/mL of streptomicin. Cells were cultured at 37° for 16 h with 5% of CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted wirh TRIZOL reagent according to manufacturer's instructions. Samples were treated with DNAase for 10 min at 37° followed by clean up using the RNeasy Kit from Qiagen following the recommended protocol.
|
| Label |
biotin
|
| Label protocol |
Biotin-labeled cRNA samples were made using Affymetrix GeneChip Expression 3'-Amplification Reagents (One-Cycle Target Labeling and Control Reagents package) according to the manufacturer's instructions.
|
| |
|
| Hybridization protocol |
Purified, fragmented cRNA was hybridized to Affymetrix's Bovine Array using Affymetrix's GeneChip Fluidics Station 450, as per Affymetrix's instructions.
|
| Scan protocol |
GeneChips were scanned using an Affymetrix GeneChip Scanner 3000
|
| Description |
Gene expression data from OFTu cells infectec with deletion mutant ORFV OV-IA82Δ024 and harvested for RNA extraction at 2 hpi
|
| Data processing |
Pre-processing was done using the GCRMA algorithm in R and Bioconductor packages using these 4 arrays plus 14 other arrays from additional mutants and time points (not released at this time). Additionally, Affymetrix's Call Detection algorithm was used to exclude probesets that were not called Present on at least one array or Marginal on two arrays from the fold-change calculation.
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| |
|
| Submission date |
Dec 10, 2009 |
| Last update date |
Mar 31, 2010 |
| Contact name |
Diego G. Diel |
| E-mail(s) |
dgdiel@illinois.edu, diegodiel@yahoo.com.br
|
| Organization name |
University of Illinois
|
| Department |
Pathobiology
|
| Street address |
2001, S Lincoln Ave
|
| City |
Urbana |
| State/province |
IL |
| ZIP/Postal code |
61802 |
| Country |
USA |
| |
|
| Platform ID |
GPL2112 |
| Series (1) |
| GSE19415 |
Expression data from primary ovine fetal turbinate cells infected with Orf Virus IA82 and deletion mutant OV-IA82Δ024 |
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