|
| Status |
Public on Dec 16, 2011 |
| Title |
MDS, 5q- Syndrome |
| Sample type |
genomic |
| |
|
| Source name |
untreated patient at diagnosis
|
| Organism |
Homo sapiens |
| Characteristics |
disease: MDS, 5q- Syndrome
tissue: bone marrow
genotype: small 12p deletions
|
| Treatment protocol |
none; samples were obtained from untreated patients at diagnosis
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Qiagen DNA extraction kit (QIAamp DNA Mini Kit; 51306); elution buffer was 10mM Tris, 0.1mM EDTA, pH 8.0
|
| Label |
Biotin
|
| Label protocol |
according to the standard Affymetrix SNP 6.0 method protocol
|
| |
|
| Hybridization protocol |
according to the standard Affymetrix SNP 6.0 method protocol
|
| Scan protocol |
according to the standard Affymetrix SNP 6.0 method protocol
|
| Data processing |
Using Genotyping Console version 3.0.1 (Affymetrix) according to the default settings for the "Copy Number / LOH Configuration" except for "Smoothing Gaussian Window". It was set to 5000 instead of 50000 and the "Smooth Log2 ratio" was selected instead of "Calibrate Smooth Log2 ratio to CN".
|
| |
|
| Submission date |
Mar 08, 2011 |
| Last update date |
Dec 16, 2011 |
| Contact name |
Hans-Ulrich Klein |
| E-mail(s) |
h.klein@uni-muenster.de
|
| Organization name |
Columbia University Medical Center
|
| Department |
Neurology
|
| Lab |
Center for Translational and Computational Neuroimmunology
|
| Street address |
622 W 168th St
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10032 |
| Country |
USA |
| |
|
| Platform ID |
GPL6801 |
| Series (1) |
| GSE27832 |
CDKN1B encoding the cyclin-dependent kinase inhibitor 1B (p27) is located in the minimally deleted region of 12p abnormalities in myeloid malignancies and its low expression is a favorable prognostic marker in acute myeloid leukemia |
|
