|
| Status |
Public on Dec 19, 2009 |
| Title |
Calu-3-H3N2-02h-1 |
| Sample type |
RNA |
| |
|
| Source name |
Calu-3, infected with H3N2, RNA collected at 2hr
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: Calu-3
cell type: bronchial epithelial cells
virus infection: H3N2
time of harvest: 2hr
|
| Treatment protocol |
Cells were infected with human influenza H3N2 and a low pathogenic avian influenza H11N9.
|
| Growth protocol |
Calu-3 cells were maintained in MEM/10% Fetal bovine serum until the day of infection. After infection, the cells were cultured in serum-free MEM.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extraction was performed by adding RLT buffer to the cells and incubated for 15min at room temp. Harvested RNA in RLT buffer was then extracted using Rneasy Mini kit (Qiagen).
|
| Label |
Cy3
|
| Label protocol |
Streptavidin-Cy3 (2ul of 1mg.mL stock per chip) was added to block E1 buffer (2ml per chip). The mix was then added to the beadchip, and incubated in dark at room temp for 10 min.
|
| |
|
| Hybridization protocol |
Standard Illumina hybridization protocol.
|
| Scan protocol |
Standard Illumina scanning protocol.
|
| Description |
H3N2-02-1
4569624067_C
|
| Data processing |
Data was imported into BeadStudio 3.0 (Illumina) and normalized to the median hybridization intensity of all genes on the beadchip, and exported to GeneSpring GX 10 (Agilent Technologies) for further analysis. Data were first normalized to the uninfected medium control, and a one-way analysis of variance (ANOVA) was used with Benjamini-Hochberg correction to identify genes that were differentially expressed in H3N2 and H11N9 infection. A p value ≤ 0.05 was considered to be significant and a fold change ≥ 2 in expression was defined as the cut-off for significant change in expression. Hierarchical clustering was performed using centroid linkage clustering with Euclidean Distance.
Non-normalized data is available in the 'GSE19580.non-normalized.txt' file, which is linked to the Series GSE19580 record as a supplementary file.
|
| |
|
| Submission date |
Dec 18, 2009 |
| Last update date |
Dec 18, 2009 |
| Contact name |
Alan Chen-Yu Hsu |
| E-mail(s) |
alan.hsu@studentmail.newcastle.edu.au
|
| Phone |
+61401784969
|
| Fax |
+61249855850
|
| Organization name |
University of Newcastle
|
| Department |
Respiratory Medicine
|
| Street address |
Lvl 3 HMRI, John Hunter Hospital, Lookout Rd, New Lambton Height
|
| City |
Newcastle |
| State/province |
NSW |
| ZIP/Postal code |
2305 |
| Country |
Australia |
| |
|
| Platform ID |
GPL8432 |
| Series (1) |
| GSE19580 |
Gene expression in Calu-3 cells after influenza H3N2 and H11N9 infection |
|
