|
| Status |
Public on Sep 12, 2011 |
| Title |
5q- syndrome before treatment 1 |
| Sample type |
RNA |
| |
|
| Source name |
5q- syndrome before treatment
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: CD14+ monocytes from peripheral blood
gender: M
age in years: 63
disease state: 5q- syndrome before treatment
karyotype: 46,XY,t(2;11)(p21;q23),del(5)(q13.3q33.3)[20]/46XY[2]
i-fish del(5)(q31): not done
transfusions: yes
treatment: baseline
|
| Extracted molecule |
total RNA |
| Extraction protocol |
CD14+ monocytes were isolated from peripheral blood. Mononuclear cells were purified by Ficoll-Hipaque density centrifugation (GE Health Care) and CD14+ cells were isolated using magnetic separation kit with specific antibodies according to manufacturer recommendations (MACS; Miltenyi Biotec). For total RNA extraction, we applied the acid guanidin-thiocyanat-phenol-chloroform method . The samples were incubated with DNase I (following manufacturer's instructions) (Qiagen). To evaluate the final integrity of total RNA, the Bioanalyzer 2100 instrument with Eukaryote Total RNA Pico Chip (both produced by Agilent Technologies) was used.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA was prepared from 200 ng of total RNA using Illumina TotalPrep RNA Amplification Kit (Ambion). In vitro transcription (IVT) was performed at 37°C for 14 hours.
|
| |
|
| Hybridization protocol |
750 ng of biotinylated cRNA was hybridized to the array for 17 hours according to the manufacturer manual. Final staining was performed with streptavidin conjugated to Cy-3 fluorescent dye.
|
| Scan protocol |
Standard Illumina scanning protocol
|
| Description |
A1
|
| Data processing |
The data were normalised using quantile normalisation with IlluminaGUI in R
|
| |
|
| Submission date |
Aug 18, 2011 |
| Last update date |
Sep 12, 2011 |
| Contact name |
Monika Belickova |
| E-mail(s) |
monika.belickova@uhkt.cz
|
| Organization name |
Institute of Hematology and Blood Transfusion
|
| Street address |
U nemocnice 1
|
| City |
Prague 2 |
| ZIP/Postal code |
128 20 |
| Country |
Czech Republic |
| |
|
| Platform ID |
GPL6883 |
| Series (1) |
| GSE31460 |
Changes in gene expression profiles in patients with 5q- syndrome in CD14+ monocytes caused by lenalidomide treatment |
|
