|
| Status |
Public on Feb 17, 2009 |
| Title |
SCC13_p53_r21 |
| Sample type |
RNA |
| |
|
| Source name |
Total RNA from human SCC13 cells infected with the p53 adenovirus for 24 hours
|
| Organism |
Homo sapiens |
| Characteristics |
keratinocyte-derived squamous cell carcinoma (SCC) cell line
|
| Treatment protocol |
SCC13 cells were infected with adenovirus as described in Lefort et al. Genes & development, 21, 562-577.
|
| Growth protocol |
Cells were grown as described in Lefort et al. Genes & development, 21, 562-577.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were collected in Tri-Reagent (Sigma) and total RNA was extracted following manufacturer’s instructions (with the exception that three rounds of chloroform extraction were performed instead of one).
|
| Label |
Cy3
|
| Label protocol |
Each sample was prepared according to the Agilent’s miRNA Microarray System protocol. 100 ng of total RNA was dephosphorylated with calf intestine alkaline phosphatase (GE Healthcare Europe GmbH, Otelfingen, Switzerland), denatured with dimethyl sulfoxide and labeled with pCp-Cy3 using T4 RNA ligase (GE Healthcare Europe GmbH, Otelfingen, Switzerland).
|
| |
|
| Hybridization protocol |
The labeled RNA was hybridized to Agilent human miRNA microarrays for 20 hours at 55°C with rotation.
|
| Scan protocol |
The arrays were scanned with an Agilent microarray scanner with high dynamic range settings as specified by the manufacturer.
|
| Description |
Biological replicate 2, technical replicate 1. Biological replicates are different adenovirus infections. Technical replicates are different labelings and hybridizations
|
| Data processing |
Agilent Feature Extraction Software was used to extract the data and different normalization procedures were applied to the Total Gene Signal intensity values
|
| |
|
| Submission date |
Jul 11, 2008 |
| Last update date |
Jan 29, 2010 |
| Contact name |
Sylvain Pradervand |
| E-mail(s) |
[email protected]
|
| Phone |
+41 21 692 39 08
|
| Organization name |
UNI Lausanne
|
| Department |
CIG
|
| Lab |
DNA Array Facility
|
| Street address |
Genopode
|
| City |
Lausanne |
| ZIP/Postal code |
1015 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL9081 |
| Series (1) |
| GSE12085 |
Impact of normalization on Agilent miRNA microarray expression profiling |
|
