|
| Status |
Public on Oct 14, 2011 |
| Title |
CLL_Peripheral_Blood_GED122 HGU133A |
| Sample type |
RNA |
| |
|
| Source name |
peripheral_blood_mononuclear cells
|
| Organism |
Homo sapiens |
| Characteristics |
life status (censoring day): 1
overall survival (days): 102
treatment status (censoring day): 0
time to treatment (days): 41
cell type: peripheral blood mononuclear cell
disease state: Chronic lymphocytic leukemia
|
| Treatment protocol |
Peripheral blood mononuclear cells from patients with chronic lymphocytic leukaemia (CLL)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Mononuclear cells from peripheral blood (PB) were enriched by Ficoll gradient centrifugation. Total RNA was isolated using the RNeasy Mini Kit (Qiagen, Hilden, Germany). cDNA preparation and in vitro transcription were performed according to standard Affymetrix protocols.
|
| Label |
biotin
|
| Label protocol |
Biotin labeling of antisense cRNA was performed according to standard Affymetrix protocols
|
| |
|
| Hybridization protocol |
Sample hybridisation was performed for 16 hours according to standard Affymetrix protocols
|
| Scan protocol |
Samples were scanned using an Affymetrix GeneChip scanner
|
| Description |
n/a
|
| Data processing |
Normalization was performed using the Robust Multichip Average (RMA) method. Quality control consisted of visual inspection of the array image for artifacts, assessment of RNA degradation plots, and inspection of rank-vs.-residual plots after normalization and probe set summarization. The 44 HG-U133 A, B chips and the 107 HG-U133 Plus 2.0 chips were normalized separately by the Robust Multichip Average (RMA) method as described by Irizarry et al 2003. Only the 44754 probe sets present on A, B chips and the 2.0 chips were included in the analysis. Some probe sets on the A, B chips tend to have lower mean signal levels and higher standard deviations than the corresponding probe sets on the Plus 2.0 chips. To eliminate this batch effect resulting from the different chip designs, we performed a second normalization using an empirical Bayesian method. This data was used in the statistical analysis. Finally we separated the normalized data for publication in GEO again. This separated normalized data is provided in the VALUE column.
|
| |
|
| Submission date |
Jul 06, 2010 |
| Last update date |
Oct 15, 2011 |
| Contact name |
Tobias Herold |
| E-mail(s) |
[email protected]
|
| Organization name |
University Hospital Grosshadern, Ludwig-Maximilians-University (LMU)
|
| Department |
Department of Internal Medicine III
|
| Street address |
Marchioninistr. 15
|
| City |
Munich |
| ZIP/Postal code |
81377 |
| Country |
Germany |
| |
|
| Platform ID |
GPL96 |
| Series (1) |
| GSE22762 |
An eight-gene expression signature for the prediction of survival and time to treatment in chronic lymphocytic leukemia |
|
| Relations |
| Reanalyzed by |
GSM628308 |
