|
| Status |
Public on Jun 08, 2010 |
| Title |
Diffuse Intrinsic Pontine Glioma 1 - Normal-250knsp |
| Sample type |
genomic |
| |
|
| Source name |
Diffuse Intrinsic Pontine Glioma 1 - Normal
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: normal brain
gender: F
age at dx (years): 5.1
os (months): 5.1
symptoms: LTS, CN
symptom duration (days): 1
tmz during rt: No
tmz post rt: No
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted from snap frozen biopsy and autopsy samples from DIPG patients using the acidic phenol-chloroform method. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer and agarose gel electrophoresis.
|
| 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
|
| Data processing |
CEL files were processed using Partek Genome Suite V6.4 and Genotyping Console V2.1 using Segmentation and Hidden-Markov Model Analysis. Tumour samples were normalized to their matched normal. Tumour samples with no corresponding matched normal were normalized using HapMap.
CHP files for samples analyzed on the 250K platform were normalized using BRLMM algorithm. CHP files for samples analyzed on the 6.0 platform were normalized using Birdseed algorithm.
Genotype Call (SNP call): AA, AB, BB, NC, and NoCall; 'Signal' = Summarized signal
|
| |
|
| Submission date |
Oct 30, 2009 |
| Last update date |
Jun 08, 2010 |
| Contact name |
Pawel Buczkowicz |
| E-mail(s) |
pawel.buczkowicz@sickkids.ca
|
| Organization name |
Hospital for Sick Children
|
| Department |
Paediatric Laboratory Medicine
|
| Lab |
BTRC
|
| Street address |
686 Bay Street
|
| City |
Toronto |
| State/province |
Ontario |
| ZIP/Postal code |
M5G 0A4 |
| Country |
Canada |
| |
|
| Platform ID |
GPL3718 |
| Series (1) |
| GSE18828 |
Affymetrix SNP array data for Diffuse Intrinsic Pontine Glioma |
|
