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Sample GSM466773 Query DataSets for GSM466773
Status Public on Jun 08, 2010
Title Diffuse Intrinsic Pontine Glioma 2 - Tumour-250knsp
Sample type genomic
Source name Diffuse Intrinsic Pontine Glioma 2 - Tumour
Organism Homo sapiens
Characteristics cell type: DIPG*
gender: F
age at dx (years): 0
os (months): 0.39
symptoms: LTS, CN
symptom duration (days): 4
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
Organization name Hospital for Sick Children
Department Paediatric Laboratory Medicine
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

Data table header descriptions

Data table
AFFX-2315060 AB 0.024686 AB 0.138751 12.091940
AFFX-2315061 AA 0.062618 AA 0.863121 11.005874
AFFX-2315062 AA 0.017508 AA 0.640433 10.043613
AFFX-2315057 AA 0.009312 AA 0.650481 9.820727
AFFX-2315058 AA 0.126360 AA 0.798543 10.800256
AFFX-2315059 AA 0.045615 AA 0.802282 10.191280
AFFX-2315063 AA 0.011785 AA 0.785591 10.000332
AFFX-2315064 AB 0.002725 AB 0.127348 10.094393
AFFX-2315065 AA 0.033860 AA 0.629789 9.387084
AFFX-2315066 BB 0.016223 BB -0.761634 10.049333
AFFX-2315067 BB 0.021900 BB -0.606053 10.727762
AFFX-2315068 AA 0.048204 AA 0.860524 10.477391
AFFX-2315069 AA 0.015245 AA 0.837898 9.976512
AFFX-2315070 BB 0.014004 BB -0.842143 10.263011
AFFX-2315071 BB 0.120918 BB -0.810473 9.737980
AFFX-2315072 AA 0.188195 AA 0.771847 10.280103
AFFX-2315073 AA 0.027320 AA 0.822732 10.576342
AFFX-2315074 AB 0.006284 AB 0.090692 9.794797
AFFX-2315075 AA 0.039636 AA 0.769816 11.017180
AFFX-2315076 AB 0.008071 AB 0.124733 10.022755

Total number of rows: 262314

Table truncated, full table size 12297 Kbytes.

Supplementary file Size Download File type/resource
GSM466773.CEL.gz 25.9 Mb (ftp)(http) CEL
GSM466773.CHP.gz 4.3 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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