|
| Status |
Public on Oct 18, 2012 |
| Title |
Cdk9 dsRNA and VSV infection at T4 hours_biological rep2 |
| Sample type |
RNA |
| |
|
| Source name |
Drosophila cells treated with Cdk9 dsRNA and infected with VSV at T4 hours, biological rep2
|
| Organism |
Drosophila melanogaster |
| Characteristics |
cell line: DL1
treatment: Cdk9 dsRNA
infection: VSV
|
| Treatment protocol |
Cells were infected with VSV (MOI 10) for 4 hours.
|
| Growth protocol |
3 million Drosophila cells (DL1) were treated with 4 ug Bgal or Cdk9 dsRNA and incubated for 3 days as described in (Cherry et al. 2005), then infected with VSV
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
|
| Label |
Biotin
|
| Label protocol |
Upon fragmentation, 100ng RNA were amplified with the Ovation RNA Amplification System v2 (NuGen), Encore Biotin Module (NuGen) was used for labeling.
|
| |
|
| Hybridization protocol |
The Standard Affymetrix hyb/wash/satining protocolwas used (Protocol FS450 002).
|
| Scan protocol |
For Scanning and Image, the GeneChip® Scanner 300) and Affymetrix® GeneChip® Command Console® Software (AGCC) were used.
|
| Description |
Gene expression data for transcript levels in Drosophila cells upon VSV infection and Cdk9 dsRNA treatment for 4 hours
|
| Data processing |
Arrays were analyzed using the Affy (Irizarry et al., 2003) and limma packages (Smyth, 2004) for R and Microsoft Excel. We calculated fold changes relative to uninfected controls and considered significant genes with at least a 2.8 fold change.
|
| |
|
| Submission date |
Oct 01, 2012 |
| Last update date |
Oct 18, 2012 |
| Contact name |
Sara Cherry |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Pennsylvania
|
| Street address |
304K Lynch Labs
|
| City |
Philadelphia |
| ZIP/Postal code |
19104 |
| Country |
USA |
| |
|
| Platform ID |
GPL1322 |
| Series (1) |
| GSE41242 |
Global analysis of Cdk9-dependence for VSV-induced genes in Drosophila cells |
|
