|
| Status |
Public on Apr 01, 2011 |
| Title |
Huh-7/IRF1 rep3 |
| Sample type |
RNA |
| |
|
| Source name |
hepatoma cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: hepatoma cells
cell line: Huh-7
transfection: IRF1
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Extraction of total cellular RNA was carried out with Qiagen Rneasy Kit according to manufactuer's recommendations.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays
|
| |
|
| Hybridization protocol |
Standard Illumina hybridization protocol
|
| Scan protocol |
Standard Illumina scanning protocol
|
| Description |
replicate 3
|
| Data processing |
The raw data was extracted using Illumina BeadStudio software without normalization. For normalization in GeneSpring, the threshold raw signal was set to 1.0 and the global normalization algorithm (percentile shift) was used with a percentile target of 75. This normalized data was used for statistical analysis, in which our IRF1-expressing cell lines were compared to control. There were 3 biological replicates for each condition. We used student's unpaired t-test to identify genes that had were significantly (p<0.05) changed in expression levels. We then selected a cutoff of 3.0 fold (upregulated) and presented the absolute fold change for this subset of genes in our publication.
|
| |
|
| Submission date |
Jan 24, 2011 |
| Last update date |
Apr 01, 2011 |
| Contact name |
Charles Rice |
| E-mail(s) |
ricec@rockefeller.edu
|
| Phone |
212-327-7046
|
| Fax |
212-327-7048
|
| Organization name |
The Rockefeller University
|
| Department |
Virology and Infectious Disease
|
| Street address |
1230 York Ave
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10065 |
| Country |
USA |
| |
|
| Platform ID |
GPL10558 |
| Series (1) |
| GSE26817 |
Impact of IRF1 on transcriptome changes in Huh-7 human hepatoma cells and STAT1-deficient human fibroblasts |
|
