|
| Status |
Public on Aug 10, 2014 |
| Title |
H5N3 H5N2-F59 F189 at 0H, biological rep1 |
| Sample type |
RNA |
| |
|
| Source name |
Mock infected MDCK rep 1
|
| Organism |
Canis lupus familiaris |
| Characteristics |
cell type: Mardin-Darby Canine Kidney cells
cell line: MDCK
infection: mock
time: control
|
| Treatment protocol |
The cells were infected with A/duck/Malaysia/F59/04/1998(H5N2) in DMEM + Glutamax (Gibco) with 2% Fetal Bovine Serum (FBS) and 100 units/ml of Penicillin/Sreptomycin (Gibco), at 37˚C, 5% CO2
|
| Growth protocol |
The cells were grown in DMEM + Glutamax (Gibco) with 10% Fetal Bovine Serum (FBS) and 100 units/ml of Penicillin/Sreptomycin (Gibco), at 37˚C, 5% CO2
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extraction was performed using RNAeasy MiniKit (Qiagen) according to the manufacturer's instruction at 4˚C
|
| Label |
biotin
|
| Label protocol |
Biotinylated mRNA were prepared according to the standard Affymetrix protocol from 150 ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
|
| |
|
| Hybridization protocol |
Following fragmentation, 15 ug of aRNA were hybridized for 16 hr at 45˚C on Canine Genome Array 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
|
| Scan protocol |
GeneChips were scanned using the Affymetrix GeneChip Scanner 3000
|
| Description |
Gene expression data from mock infected MDCK rep 1
|
| Data processing |
The data were analyzed with GeneChip Operating Software 5.0 (GCOS 5.0) using Affymetrix default analysis settings. Further analysis was done in GeneSpring 11.0. The normalization was done using internal and external control genes as assigned by Affymetrix. The target intensity of each array on a given time point was first filtered by the flagging of Present (P) in 3 replicates at one time-point, which then further calculated in fold change up- or downregulation with respect to the signal intensity in MOCK infected cells, after analyzed by ANOVA with p value ≤ 0.05.
|
| |
|
| Submission date |
Aug 18, 2011 |
| Last update date |
Aug 10, 2014 |
| Contact name |
Richard J Sugrue |
| E-mail(s) |
RJSUGRUE@ntu.edu.sg
|
| Organization name |
Nanyang Technological University
|
| Department |
Divison of Molecular and Cell Biology
|
| Street address |
60 Nanyang Drive
|
| City |
Singapore |
| ZIP/Postal code |
637551 |
| Country |
Singapore |
| |
|
| Platform ID |
GPL3738 |
| Series (4)
|
| GSE31513 |
Host cell gene expression in Influenza A/duck/Malaysia/F59/04/1998 (H5N2) infected MDCK cells at 10 hour post infection |
| GSE31514 |
Host cell gene expression in Influenza A/duck/Malaysia/F189/07/2004 (H5N2) infected MDCK cells at 10 hour post infection |
| GSE31516 |
Host cell gene expression in Influenza A/duck/Malaysia/F119/3/1997 (H5N3) infected MDCK cells at 10 hour post infection |
| GSE31524 |
Host cells infected by various types of viruses |
|
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