|
| Status |
Public on Jan 20, 2009 |
| Title |
exp.n 22 atra Y atorvastatin N time 48 h |
| Sample type |
RNA |
| |
|
| Source name |
NB4 human APL cell line
|
| Organism |
Homo sapiens |
| Characteristics |
NB4 human APL cell line
|
| Treatment protocol |
NB-4 cells were pretreated for one hour with ATRA, then treated with atorvastatin at times indicated in Title field
|
| Growth protocol |
NB4 human APL cell line was grown in RPMI 1640 supplemented with 10% fetal bovine serum and antibiotics.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction as recomanded by manufacturer
|
| Label |
Biotin
|
| Label protocol |
cRNA was synthesized using Illumina RNA Amplification Kit Ambion (Austin, TX) starting from 500 ng of total RNA and following the procedure suggested by manufacturer.
|
| |
|
| Hybridization protocol |
Sentrix® Human-6 Expression BeadChip hybridization, washing and staining were also done as suggested by the manufacturer.
|
| Scan protocol |
Arrays were scanned on Illumina BeadStation 500
|
| Description |
BeadChip array data quality control was performed using Illumina BeadStudio software version 1.3.1.5. Probe average intensity signal was calculated with
BeadStudio without background correction. Raw data were analyzed with Bioconductor. To remove low quality signals two filters were applied sequentially to the 47293 reference sequences available in the Sentrix® Human-6 Expression BeadChip: gene specific detection value should be ≥0.6 in at least 50% of the samples, gene specific interquantile range should be ≥0.2. The statistical analysis of the time course experiments was performed using maSigPro Bioconductor library.
|
| Data processing |
Average probe intensities were log2 transformed and normalized by loess method.
|
| |
|
| Submission date |
Sep 18, 2008 |
| Last update date |
Jan 20, 2009 |
| Contact name |
Raffaele A Calogero |
| E-mail(s) |
raffaele.calogero@unito.it
|
| Phone |
++39 0116706454
|
| Organization name |
University of Torino
|
| Department |
Molecular Biotechnology Center
|
| Lab |
Bioinformatics and Genomics Unit
|
| Street address |
Via Nizza 52
|
| City |
Torino |
| State/province |
To |
| ZIP/Postal code |
10126 |
| Country |
Italy |
| |
|
| Platform ID |
GPL2507 |
| Series (1) |
| GSE12870 |
Regulation of leukemic cell differentiation and retinoid-induced gene expression by statins |
|
