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Sample GSM466782 Query DataSets for GSM466782
Status Public on Jun 08, 2010
Title Diffuse Intrinsic Pontine Glioma 11 - Tumour-250knsp
Sample type genomic
Source name Diffuse Intrinsic Pontine Glioma 11 - Tumour
Organism Homo sapiens
Characteristics cell type: DIPG
gender: M
age at dx (years): 1.66
os (months): **
symptoms: LTS, ataxia, CN
symptom duration (days): 30
tmz during rt: No
tmz post rt: No
other chemo: 99703 then focal radiation1
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 0.012291 AB 0.048201 11.412597
AFFX-2315061 BB 0.015376 BB -0.836440 10.480065
AFFX-2315062 AB 0.180436 AB -0.388877 10.222439
AFFX-2315057 AB 0.023541 AB -0.237723 10.791469
AFFX-2315058 AA 0.076665 AA 0.800722 11.313148
AFFX-2315059 AA 0.011401 AA 0.806670 9.978593
AFFX-2315063 BB 0.033559 BB -0.840803 10.464304
AFFX-2315064 AB 0.015063 AB 0.235857 9.916731
AFFX-2315065 BB 0.300152 BB -0.551221 9.738984
AFFX-2315066 BB 0.024765 BB -0.791748 9.954594
AFFX-2315067 NC 0.803341 BB -0.372082 10.717299
AFFX-2315068 AB 0.002730 AB 0.075829 9.974052
AFFX-2315069 AA 0.003367 AA 0.762932 9.671140
AFFX-2315070 BB 0.022314 BB -0.847971 10.187543
AFFX-2315071 NC 0.702254 AB -0.579896 9.445347
AFFX-2315072 AA 0.131868 AA 0.625020 10.500537
AFFX-2315073 AA 0.044133 AA 0.733884 10.236337
AFFX-2315074 BB 0.093064 BB -0.779795 9.506989
AFFX-2315075 AA 0.117937 AA 0.765162 10.829070
AFFX-2315076 AB 0.003221 AB -0.002015 9.964477

Total number of rows: 262314

Table truncated, full table size 12289 Kbytes.

Supplementary file Size Download File type/resource
GSM466782.CEL.gz 24.9 Mb (ftp)(http) CEL
GSM466782.CHP.gz 4.3 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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