|
| Status |
Public on Feb 10, 2013 |
| Title |
H295R_control_replicate 3 |
| Sample type |
RNA |
| |
|
| Source name |
H295R cell line, 24h, control, replicate 3
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: H295R
treatment: none
|
| Treatment protocol |
Cells were treated for 24h with 9cisRA at a final concentration of 2.5*10-5, 5*10-5 and 7.5*10-5 M dissolved in absolute ethanol. The control groups were treated with the same amount of ethanol.
|
| Growth protocol |
For the gene expression H295R expreiment 2*10^6 cells were grown in a 12,5cm2 cell sulture flask / samples
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from 2*10^6 9cisRA treated and control cells with Qiagen miRNeasy Mini Kit and Rnase-Free Dnase Set according to the manufacture's protocol (Qiagen GmbH, Hilden, Germany). RNA concentration was measured by NanoDrop 1000 Spectrophotometer (Thermo Fisher Scientific Inc., Waltham, MA, USA) and RNA integrity was determined by an Agilent 2100 Bioanalyzer System (Agilent Technologies Inc., Santa Clara, CA, USA). Samples with an RNA integrity number (RIN) above 8.0 were used for further analysis.
|
| Label |
Cy3
|
| Label protocol |
Total RNA (200 ng) was labeled with Cy3 and amplified using Low Input Quick Amp Labeling Kit according to the instructions of the manufacturer.
|
| |
|
| Hybridization protocol |
Labeled RNA was purified and hybridized to Agilent Whole Human Genome Microarray slides, according to the manufacturer’s protocol.
|
| Scan protocol |
After washing, array scanning and feature extraction was performed with default scenario by Agilent DNA Microarray Scanner and Feature Extraction Software 9.5.3.
|
| Description |
Gene expression after 24hr in control H295R cells
|
| Data processing |
Total gene signal normalization at the 75th percentile of raw signal values and baseline transformation at the median of all samples was performed by GeneSpring software 10.1 following Agilent's recommendation. Genes were filtered by flag values (100% of samples are present or marginal in at least one group) and raw data (expression is higher than 20 percentile in the 100% of samples in at least one group). Fold change filter was set to 2-fold between 9-cisRA-treated groups versus control cells.
|
| |
|
| Submission date |
Dec 20, 2012 |
| Last update date |
Feb 10, 2013 |
| Contact name |
Diana Rita Szabo |
| Organization name |
Semmelweis University
|
| Street address |
Szentkirályi u. 46
|
| City |
Budapest |
| ZIP/Postal code |
H-1088 |
| Country |
Hungary |
| |
|
| Platform ID |
GPL6480 |
| Series (1) |
| GSE43090 |
Exression profiling of 9-cisRA in adrenocortical carcinoma cell line |
|
