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Sample GSM466778 Query DataSets for GSM466778
Status Public on Jun 08, 2010
Title Diffuse Intrinsic Pontine Glioma 7 - Tumour-250knsp
Sample type genomic
Source name Diffuse Intrinsic Pontine Glioma 7 - Tumour
Organism Homo sapiens
Characteristics cell type: DIPG
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_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 AA 0.016151 AA 0.756988 11.756323
AFFX-2315061 NC 0.531943 BB -0.589880 10.394156
AFFX-2315062 AA 0.241575 AA 0.428356 9.776596
AFFX-2315057 AB 0.011188 AB -0.115431 10.170858
AFFX-2315058 AA 0.012768 AA 0.772616 11.074733
AFFX-2315059 AA 0.020625 AA 0.820062 10.017154
AFFX-2315063 AB 0.001654 AB -0.109928 10.220595
AFFX-2315064 AB 0.009118 AB 0.082165 9.981213
AFFX-2315065 AB 0.007604 AB -0.199822 9.584605
AFFX-2315066 BB 0.013918 BB -0.743753 9.755354
AFFX-2315067 AB 0.034913 AB -0.118279 10.937265
AFFX-2315068 AA 0.003246 AA 0.819599 10.186071
AFFX-2315069 AA 0.011553 AA 0.838011 9.926818
AFFX-2315070 AB 0.000285 AB -0.138014 10.271834
AFFX-2315071 AB 0.004579 AB 0.012191 9.173859
AFFX-2315072 AA 0.130597 AA 0.802160 10.593526
AFFX-2315073 AB 0.001552 AB 0.239560 10.274746
AFFX-2315074 BB 0.154070 BB -0.692635 9.183713
AFFX-2315075 AB 0.006717 AB 0.237463 10.953385
AFFX-2315076 BB 0.044085 BB -0.640539 9.876293

Total number of rows: 262314

Table truncated, full table size 12289 Kbytes.

Supplementary file Size Download File type/resource
GSM466778.CEL.gz 25.2 Mb (ftp)(http) CEL
GSM466778.CHP.gz 4.3 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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