|
| Status |
Public on Jan 01, 2010 |
| Title |
pIC 4h |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
SK-Mel-103 Control 4h
|
| Organism |
Homo sapiens |
| Characteristics |
SK-Mel-103 Time: 4h
|
| Treatment protocol |
1ug/ml of pIC or 1ug/ml pIC coupled with PEI
|
| Growth protocol |
Dulbecco’s modified Eagle’s medium (Life Technologies, Rockville, MD, USA) supplemented with 10% fetal bovine serum (Nova-Tech Inc., Grand Island, NY, USA) penicillin (100 U/ml), streptomycin (100 U/ml)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extracted using Qiagen Rneasy mini kit following manufacturer's instructions
|
| Label |
Cy3
|
| Label protocol |
Cy3 NT Cy5 treated (pIC/PEI-pIC)
|
| |
|
| Channel 2 |
| Source name |
pIC treated SK-Mel-103 4h
|
| Organism |
Homo sapiens |
| Characteristics |
SK-Mel-103 treated with 1ug/ml of polyinosine-polycytidylic acid Age: 4 hours
|
| Treatment protocol |
1ug/ml of pIC or 1ug/ml pIC coupled with PEI
|
| Growth protocol |
Dulbecco’s modified Eagle’s medium (Life Technologies, Rockville, MD, USA) supplemented with 10% fetal bovine serum (Nova-Tech Inc., Grand Island, NY, USA) penicillin (100 U/ml), streptomycin (100 U/ml)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extracted using Qiagen Rneasy mini kit following manufacturer's instructions
|
| Label |
Cy5
|
| Label protocol |
Cy3 NT Cy5 treated (pIC/PEI-pIC)
|
| |
|
| |
| Hybridization protocol |
Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential
|
| Scan protocol |
Images were quantified using Agilent Feature Extraction Software
|
| Description |
SK-Mel-103 treated 4 hours with 1ug/ml of polyinosine-polycytidylic acid
|
| Data processing |
Background substraction were carried out using normexp. Lowess method for within array normalization and quantiles method for between array normalization were performed. Differentially expressed genes were obtained by using R limma package (Smyth et al., 2005) from Bioconductor project (http://www.bioconductor.org). Smyth GK, Michaud J and Scott HS. (2005). Use of within-array replicate spots for assessing differential expression in microarray experiments. Bioinformatics 21: 2067-2075.
|
| |
|
| Submission date |
Jan 15, 2009 |
| Last update date |
Jan 15, 2009 |
| Contact name |
Maria S Soengas |
| E-mail(s) |
msoengas@cnio.es
|
| Organization name |
Spanish National Cancer Research Institute
|
| Department |
Molecular Pathology
|
| Lab |
Melanoma
|
| Street address |
Melchor Fernandez Almagro, 3
|
| City |
Madrid |
| ZIP/Postal code |
28029 |
| Country |
Spain |
| |
|
| Platform ID |
GPL6480 |
| Series (1) |
| GSE14445 |
Melanoma SK-Mel-103 cell line : control vs. treated with pIC/pIC+PEI |
|
