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Status |
Public on Sep 12, 2011 |
Title |
5q- syndrome before treatment 5 |
Sample type |
RNA |
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|
Source name |
5q- syndrome before treatment
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Organism |
Homo sapiens |
Characteristics |
cell type: CD14+ monocytes from peripheral blood gender: M age in years: 55 disease state: 5q- syndrome before treatment karyotype: 46,XY[15] i-fish del(5)(q31): 54 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.
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|
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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.
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Scan protocol |
Standard Illumina scanning protocol
|
Description |
A5
|
Data processing |
The data were normalised using quantile normalisation with IlluminaGUI in R
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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 |
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