|
| Status |
Public on Sep 02, 2009 |
| Title |
Hyperdip50-SNP-#39-250ksty |
| Sample type |
genomic |
| |
|
| Source name |
Pediatric acute lymphoblastic leukemia (ALL) blast samples or reference leukemic blast samples.
|
| Organism |
Homo sapiens |
| Characteristics |
Leukemic blasts from 242 pediatric acute lymphoblastic leukemia (ALL) patients, or reference leukemic blast samples used for DNA copy number analysis.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted from mononuclear cell preparations of leukemic blasts obtained from peripheral blood or bone marrow at diagnosis using the Qiagen DNA Blood Mini Kit. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer, PicoGreen and agarose gel electrophoresis.
|
| Label |
Biotin
|
| |
|
| 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 |
242 pediatric acute lymphoblastic leukemia blast samples were analyzed.
|
| Data processing |
CEL files were generated using GeneChip Operating Software v 3.0 and SNP calls generated using GeneChip DNA Analysis Software (GDAS) v 3.0 or Affymetrix GeneChip Genotyping Analysis Software (GTYPE) v 4.0. The summary files (containing both expression values and SNP calls) were generated by dChipSNP, and a modified array normalization algorithm that accounts for gross cytogenetic abnormalities in the blast samples (described in the paper).
|
| |
|
| Submission date |
Aug 14, 2006 |
| Last update date |
Dec 22, 2009 |
| Contact name |
Charles G Mullighan |
| E-mail(s) |
charles.mullighan@stjude.org
|
| Phone |
1-901-595-3387
|
| Organization name |
St Jude Children's Research Hospital
|
| Department |
Pathology
|
| Street address |
262 Danny Thomas Place
|
| City |
Memphis |
| State/province |
TN |
| ZIP/Postal code |
38105 |
| Country |
USA |
| |
|
| Platform ID |
GPL3720 |
| Series (1) |
| GSE5511 |
Genes regulating B cell development are mutated in acute lymphoid leukaemia |
|
