|
| Status |
Public on Apr 28, 2011 |
| Title |
Chronic Lymphocytic Leukemia_diagnostic sample_patient SCAN3 |
| Sample type |
genomic |
| |
|
| Source name |
CLL cells from periferal blood sample
|
| Organism |
Homo sapiens |
| Characteristics |
hiearchical model of known recurrent aberrations: del(11q)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted from mononuclear cell preparations of obtained from peripheral blood at diagnosis using the Qiagen DNA Blood Mini Kit. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer.
|
| Label |
Biotin
|
| Label protocol |
As per manufacturer (Affymetrix)
|
| |
|
| Hybridization protocol |
DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.
|
| Scan protocol |
The Arrays were washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.
|
| Data processing |
Quality control (QC), genotype calling and probe level normalization were performed in the Affymetrix GeneChip® Genotyping Analysis Software (GTYPE) 4.1. The Dynamic Model (DM) algorithm was used to perform single sample QC and genotype calls were made using BRLMM (34). Copy number normalization was performed in order to produce log2ratios using the Copy Number Analysis Tool (CNAT) 4.0.1. Eighty-two normal samples analyzed at the Uppsala Array Platform were used as reference set.
Standard Affymetrix CNCHP files with Log2 probe intenisities relative to reference
|
| |
|
| Submission date |
Mar 17, 2011 |
| Last update date |
Apr 28, 2011 |
| Contact name |
Anders Isaksson |
| E-mail(s) |
anders.isaksson@medsci.uu.se
|
| Organization name |
Uppsala University
|
| Street address |
Akademiska sjukhuset ing61 3tr
|
| City |
Uppsala |
| ZIP/Postal code |
75185 |
| Country |
Sweden |
| |
|
| Platform ID |
GPL3718 |
| Series (1) |
| GSE28030 |
Affymetrix SNP array data for Chronic Lymphocytic Leukemia_diagnostic sample_patient samples |
|
