|
| Status |
Public on Sep 27, 2012 |
| Title |
CLL with unmutated IgV gene uCLL_2 |
| Sample type |
RNA |
| |
|
| Source name |
human peripheral blood
|
| Organism |
Homo sapiens |
| Characteristics |
tumor stage: tumor
cell type: CLL cell with unmutated IgV gene
|
| Growth protocol |
cell sorting, see sample title
|
| Extracted molecule |
total RNA |
| Extraction protocol |
10,000 cell samples sorted into Trizol lysis buffer, hydrous phase mixed with equal volume of 70% EtOH and loaded onto Qiagen RNeasy micro colum. Further processing according to manufacturer's instruction.
|
| Label |
biotin
|
| Label protocol |
Two rounded in vitro transcription protocol with Ambion MessageAmpII kit and MessageAmp Biotin Enhanced-Kit according to manufacturer's instructions.
|
| |
|
| Hybridization protocol |
Following fragmentation, cRNA was hybridized on GPL570 Arrays with the Affymetrix GeneChip Hybridization, Wash and Stain kit, according to manufacturer's instructions.
|
| Scan protocol |
GeneChips were scanned using the Affymetrix GeneChip Scanner 7G and GeneChip Command Console 3.2 software.
|
| Description |
batch 3
|
| Data processing |
Data were normalized according to vsn and imported into Gene Spring GX 7.3.1 and filtered according to a minimum amount of 4 present calls (according to GC-RMA normalization and flagging by MAS5) within at least one condition (cell type) and raw signal above 50. Remaining probe sets were exported, processed with ComBat software to compell batch effects and reimported into Gene Spring for further analysis.
|
| |
|
| Submission date |
Mar 28, 2012 |
| Last update date |
Sep 27, 2012 |
| Contact name |
Marc JS Seifert |
| E-mail(s) |
marc.seifert@uni-due.de
|
| Organization name |
University Hospital Essen
|
| Department |
IFZ
|
| Lab |
AGII
|
| Street address |
Virchowstraße 173
|
| City |
Essen |
| State/province |
NRW |
| ZIP/Postal code |
45122 |
| Country |
Germany |
| |
|
| Platform ID |
GPL570 |
| Series (1) |
| GSE36907 |
Cellular Origin and Pathophysiology of Chronic Lymphocytic Leukemia |
|
