|
| Status |
Public on Dec 22, 2009 |
| Title |
DiploidRef-Jan-1 (250K_Nsp_SNP) |
| Sample type |
genomic |
| |
|
| Source name |
Normal brain tissue
|
| Organism |
Homo sapiens |
| Characteristics |
histology: Normal
age (months): NA
gender: female
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Standard phenol-chloroform extraction
|
| Label |
biotin
|
| Label protocol |
Biotinylated DNA was prepared according to the standard Affymetrix protocol from 250 ng genomic DNA (Genechip Mapping 500k assay manual 701930 Rev.3, Affymetrix).
|
| |
|
| Hybridization protocol |
Hybridizations were performed according to the standard Affymetrix protocol from 250 ng genomic DNA (Genechip Mapping 500k assay manual 701930 Rev.3, Affymetrix) using an Affymetrix hybridisation oven 640 and an Affymetrix Fluidic station 450.
|
| Scan protocol |
Scanning performed according to the standard Affymetrix protocol from 250 ng genomic DNA (Genechip Mapping 500k assay manual 701930 Rev.3, Affymetrix) using an Affymetrix scanner 3000.
|
| Description |
no additional information
|
| Data processing |
Affymetrix CEL files were generated using the Affymetrix Genotyping Analysis Software (GTYPE 4.1). The CEL files and corresponding SNP genotype cell files were imported into dChip, normalized and modeled. Probe intensity data for each array were normalized using the invariant set method, and model-based expression was performed using the perfect-match/mismatch (PM/MM) model to summarize signal intensities for each probe set. (DNA copy number was inferred by comparing the signal intensity of each SNP probe set for each tumor sample against a diploid reference set of 39 samples, with subsequent median smoothing over a window size of 10.)
|
| |
|
| Submission date |
Dec 22, 2008 |
| Last update date |
Feb 23, 2009 |
| Contact name |
David J. H. Shih |
| E-mail(s) |
david.shih@utoronto.ca
|
| Phone |
(416) 813-7654
|
| Organization name |
Hospital for Sick Children
|
| Department |
Developmental and Stem Cell Biology
|
| Lab |
Peter Gilgan Centre for Research and Learning
|
| Street address |
686 Bay St
|
| City |
Toronto |
| State/province |
ON |
| ZIP/Postal code |
M5G 0A4 |
| Country |
Canada |
| |
|
| Platform ID |
GPL3718 |
| Series (2) |
| GSE14087 |
Genotype profiling of primitive neuroectodermal tumours (250K_Nsp_SNP and 250K_Sty_SNP) |
| GSE14296 |
Genotype and expression profiling of primitive neuroectodermal tumours |
|
