|
| Status |
Public on Dec 01, 2009 |
| Title |
AML_132_D_Nsp |
| Sample type |
genomic |
| |
|
| Source name |
bone marrow
|
| Organism |
Homo sapiens |
| Characteristics |
sample: Acute myeloid leukemia diagnosis sample
cell type: mononuclear cells
disease state: Acute myeloid leukemia
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted from mononuclear cells preparations obtained from peripheral blood using using the Qiagen ALL-Prep DNA/RNA 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 then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.
|
| Description |
Hybridized to 250K_Nsp
Genotype Call (SNP call): AA, AB, BB, NC, and NoCall; 'Signal' = Summarized signal
|
| Data processing |
1) CEL files and CHP files (generated by Affymetrix GTYPE) were processed by Copy Number Analyzer for GeneChip (CNAG) version 2.0 software or 2)CEL files and TXT files (generated by Affymetrix GTYPE using the DM algorithm) were processed by dChip and model-based expression performed using the PM/MM model. Normalization was performed using the reference normalization algorithm developed at St Jude and described in Mullighan et al Nature 2007;446:758. Normalization was performed against bone marrow or peripheral blood samples at remission from the same patient (paired analysis).
|
| |
|
| Submission date |
Nov 18, 2009 |
| Last update date |
Nov 30, 2009 |
| Contact name |
Jan Kroenke |
| E-mail(s) |
jankroenke@gmx.de
|
| Organization name |
University Hospital of Ulm
|
| Department |
Department of Internal Medicine III
|
| Lab |
Molecular Genetics of Myeloid Leukemia
|
| Street address |
Albert-Einstein-Allee 23
|
| City |
Ulm |
| ZIP/Postal code |
89081 |
| Country |
Germany |
| |
|
| Platform ID |
GPL3718 |
| Series (1) |
| GSE19101 |
Identification of Acquired Copy Number Alterations and Uniparental Disomies in Cytogenetically Normal AML |
|
