|
| Status |
Public on Dec 10, 2008 |
| Title |
6_Affymetrix |
| Sample type |
genomic |
| |
|
| Source name |
Blood
|
| Organism |
Homo sapiens |
| Characteristics |
Gender: Female, Tumor content: 69%
|
| 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 the Affymetrix GeneChip® Genotyping Analysis Software (GTYPE) 4.1. The Dynamic Model (DM) algorithm was used to perform single sample QC. The QC specification for 250K is a Call Rate > 93% using the algorithm defaults. Genotype calls were made using the BRLMM algorithm. Parameter settings(CNAT 4.0.1): Transition decay 5 Mb, Median normalization and 0Mb smoothing factor. The reference set used consisted of 96 CEU samples from the HapMap project (www.hapmap.org/downloads/raw_data/affy500k/).
|
| |
|
| Submission date |
Oct 28, 2008 |
| Last update date |
Dec 10, 2008 |
| Contact name |
Richard Rosenquist Brandell |
| E-mail(s) |
richard.rosenquist@genpat.uu.se
|
| Organization name |
Uppsala University
|
| Department |
Genetics and Pathology
|
| Street address |
Rudbeck Laboratory
|
| City |
Uppsala |
| ZIP/Postal code |
SE-751 85 |
| Country |
Sweden |
| |
|
| Platform ID |
GPL3718 |
| Series (1) |
| GSE13557 |
Screening for copy-number alterations and LOH in CLL - a comparative study of four microarray platforms |
|
