|
| Status |
Public on Sep 02, 2009 |
| Title |
Other-SNP-#5-remission-50kxba |
| Sample type |
genomic |
| |
|
| Source name |
Remission samples.
|
| Organism |
Homo sapiens |
| Characteristics |
Remission samples that correspond to those tumor samples that have copy number abnormalities in specific genes.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA from remission samples was extracted by the Qiagen method or phenol/Chloroform. 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 |
Leukemia remission samples that correspond to those leukemia blast samples that have specific genetic lesions.
|
| 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 |
GPL2005 |
| Series (1) |
| GSE5511 |
Genes regulating B cell development are mutated in acute lymphoid leukaemia |
|
