|
| Status |
Public on Nov 23, 2009 |
| Title |
SCAN404 |
| Sample type |
genomic |
| |
|
| Source name |
Blood
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Blood
phenotype: CLL sample
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Extraction of genomic DNA was performed using QIAamp DNA Mini kit (Qiagen) according to the manufacturer's instructions.
|
| Label |
Total genomic DNA was digested with a restriction enzyme (Nsp1), ligated to an appropriate adapter for the enzyme, and subjected to PCR amplification using a single primer
|
| Label protocol |
After digestion with DNase I, the PCR products were labeled with a biotinylated nucleotide analogue using terminal deoxynucleotidyl transferase and hybridized to the microarray
|
| |
|
| Hybridization protocol |
Hybridized probes were captured by streptavidin-phycoerythrin conjugates using Fluidics Station 450
|
| Scan protocol |
GeneChip Scanner 3000 7G (Affymetrix Inc., Santa Clara, CA)
|
| Description |
Array experiments were performed according to the standard protocols for Affymetrix GeneChip Mapping 250K arrays (Gene Chip Mapping 500K Assay Manual (P/N 701930 Rev2.), Affymetrix Inc., Santa Clara, CA).
|
| Data processing |
QC, genotype calling and log2 ratios were produced in Affymetric Genotyping Console 3.0.1. The Dynamic Model (DM) algorithm was used to perform single sample QC. The QC specification for 250K is a Call Rate > 93
|
| |
|
| Submission date |
Jun 03, 2009 |
| Last update date |
Nov 23, 2009 |
| 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) |
| GSE16406 |
Copy-number alterations correlate to high-risk genomic aberrations and survival in chronic lymphocytic leukemia |
|
