|
| Status |
Public on Dec 31, 2010 |
| Title |
Patient_25 at diagnosis |
| Sample type |
genomic |
| |
|
| Source name |
Dx bone marrow
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: bone marrow
leukemia type: Normal Karyotype-Acute Myeloid Leukemia
disease stage: diagnosis
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA (gDNA) was extracted from bone marrow cells at the diagnosis (Dx samples; blasts >90%) and at the first complete remission phase (R samples; <5% blasts at morphological evaluation) using the QIAamp DNA Blood Mini Kit according to the manufacturer’s instructions. The concentration and the quality of the DNA were determined using NanoDrop spectrophotometer.
|
| Label |
biotin
|
| Label protocol |
Amplification and labeling were performed according to the protocol supplied by the Affymetrix for SNP 6.0 arrays. 500 ng of gDNA was digested with NspI and StyI restriction enzymes, ligated to respectively NspI and StyI adaptors, amplified by PCR using a single primer. PCR products were purified and the amplicons were quantified using a NanoDrop spectrophotometer. 40-70 µg of purified amplicons were fragmented and biotin end-labeled
|
| |
|
| Hybridization protocol |
Biotin-labeled fragments were hybridized to a Genechip Affymetrix SNP 6.0 arrays at 50°C for 16-18 hours in a GeneChip® Hybridization Oven 640 (Affymetrix, Inc.). Washing and staining with streptavidin-phycoerthrin was performed in a GeneChip® Fluidics Station 450 (Affymetrix, Inc.).
|
| Scan protocol |
Arrays were scanned with a GeneChip® Scanner 3000 7G (Affymetrix, Inc.) and raw data processing was performed using the “GeneChip Operating Software”.
|
| Description |
AML25Dx exp9
|
| Data processing |
Data processing was performed by the software "Genotyping Console v3.0.1 ". The following algorithms were used: 1) SNP 6.0 Birdseed v2 algorithm for genotyping, 2) BRLMM-P-Plus algorithm and Hidden Markov Model with regional GC correction for copy number analysis, 3) the LOH algorithm (CN5).
|
| |
|
| Submission date |
May 11, 2010 |
| Last update date |
Dec 31, 2010 |
| Contact name |
Vincenza Barresi |
| E-mail(s) |
barregi@unict.it
|
| Organization name |
University of Catania
|
| Street address |
V.le A Doria, 6
|
| City |
Catania |
| ZIP/Postal code |
95125 |
| Country |
Italy |
| |
|
| Platform ID |
GPL6801 |
| Series (1) |
| GSE21780 |
SNP arrays in matched diagnosis/remission samples of normal karyotype-acute myeloid leukemia |
|
