|
| Status |
Public on Sep 01, 2010 |
| Title |
GE 99 |
| Sample type |
RNA |
| |
|
| Source name |
Human B-cell chronic lymphocytic leukemia patient GE99
|
| Organism |
Homo sapiens |
| Characteristics |
legend: VH status = IgVH mutational status (Fais et al. J Clin Invest, 1998)
Sex: F
vh status: unmut
disease: B-cell chronic lymphocytic leukemia (B-CLL)
Stage: Binet A
cell type: CD5/CD19/CD23 triple-positive B cells
|
| Treatment protocol |
Peripheral blood mononuclear cells from B-CLL patients were isolated by Ficoll-Hypaque (Seromed, Biochrom KG, Berlin, Germany) density-gradient centrifugation and the proportion of CD5/CD19/CD23 triple positive B cells in the suspension was determined by direct immunofluorescence performed using a FACS-sort flow cytometer (Becton Dickinson & Co, Sunnyvale, CA) with antibodies to: CD19 FITC/PE, CD23 PE and CD5 Cy-Chrome (Becton Dickinson). If B-CLL cells were less than 90%, T cells, NK cells and monocytes were removed by negative selection using CD3, CD56, CD16, and CD14 monoclonal antibody (mAb) treatment (Becton Dickinson) followed by magnetic beads (Goat Anti-Mouse IgG Dynabeads, Dynal Biotech ASA, Oslo, Norway).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction of total RNA was performed according to the manufacturer's instructions (Gibco BRL). RNA was purified using the Rneasy Mini Kit according to the manufacturer's instruction (Qiagen).
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 micrograms of total RNA (Expression Analysis Technical Manual, Affymetrix).
|
| |
|
| Hybridization protocol |
Following fragmentation, 15 micrograms of cRNA were hybridized for 16 hr and 30 minutes at 45°C on GeneChip HG-U133A Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
|
| Scan protocol |
HG-U133A arrays were scanned using the GeneChip Scanner 3000 7G (Affymetrix).
|
| Description |
Gene expression profiling data from human B-cell chronic lymphocytic leukemia patient GE99
|
| Data processing |
The probe-level signals were converted to expression values using the Bioconductor function for Robust Multi-array Analysis (RMA), in which perfect match intensities are background adjusted, normalized by means of quantile-quantile normalization, and log2 transformed.
|
| |
|
| Submission date |
Jun 22, 2009 |
| Last update date |
Sep 16, 2010 |
| Contact name |
Luca Agnelli |
| E-mail(s) |
luca.agnelli@istitutotumori.mi.it, luca.agnelli@gmail.com
|
| Phone |
+390223903581
|
| Organization name |
IRCCS Istituto Nazionale dei Tumori
|
| Department |
Department of Advanced Diagnostics
|
| Street address |
Venezian 1
|
| City |
MILAN |
| ZIP/Postal code |
20133 |
| Country |
Italy |
| |
|
| Platform ID |
GPL96 |
| Series (1) |
| GSE16746 |
Genomic approach in B-cell Chronic Lymphocytic Leukemia: molecularly distinct subgroups of patients with 13q14 deletion |
|
