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Sample GSM466787 Query DataSets for GSM466787
Status Public on Jun 08, 2010
Title Diffuse Intrinsic Pontine Glioma 7 - Normal-250knsp
Sample type genomic
Source name Diffuse Intrinsic Pontine Glioma 7 - Normal
Organism Homo sapiens
Characteristics cell type: normal brain
gender: M
age at dx (years): 4.98
os (months): 6.49
symptoms: LTS, ataxia, CN
symptom duration (days): 2
tmz during rt: Yes
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_Sty
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 AA 0.044641 AA 0.789285 11.890956
AFFX-2315061 AB 0.015762 AB -0.114675 10.649623
AFFX-2315062 AA 0.220076 AA 0.450453 9.921952
AFFX-2315057 AB 0.008061 AB -0.241230 10.178369
AFFX-2315058 AA 0.008646 AA 0.757441 11.056078
AFFX-2315059 AA 0.327872 AA 0.687155 9.509804
AFFX-2315063 AB 0.007843 AB -0.194061 10.502610
AFFX-2315064 AB 0.036556 AB 0.351844 9.974241
AFFX-2315065 AB 0.005131 AB -0.215519 9.759625
AFFX-2315066 BB 0.014378 BB -0.758878 9.806978
AFFX-2315067 AB 0.078160 AB -0.106300 11.293281
AFFX-2315068 AA 0.048191 AA 0.759560 9.913421
AFFX-2315069 AA 0.020687 AA 0.777853 9.519951
AFFX-2315070 AB 0.009808 AB -0.025052 9.955583
AFFX-2315071 AB 0.107152 AB -0.381326 9.115329
AFFX-2315072 AA 0.156198 AA 0.597219 10.378080
AFFX-2315073 AB 0.000352 AB 0.181538 10.363555
AFFX-2315074 BB 0.004357 BB -0.748957 9.727921
AFFX-2315075 AB 0.111072 AB 0.214204 10.419435
AFFX-2315076 BB 0.001316 BB -0.572321 9.885172

Total number of rows: 262314

Table truncated, full table size 12284 Kbytes.

Supplementary file Size Download File type/resource
GSM466787.CEL.gz 23.0 Mb (ftp)(http) CEL
GSM466787.CHP.gz 4.3 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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