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Sample GSM466775 Query DataSets for GSM466775
Status Public on Jun 08, 2010
Title Diffuse Intrinsic Pontine Glioma 4 - Tumour-250knsp
Sample type genomic
Source name Diffuse Intrinsic Pontine Glioma 4 - Tumour
Organism Homo sapiens
Characteristics cell type: DIPG
gender: M
age at dx (years): 10.64
os (months): 10.16
symptoms: LTS, ataxia, CN
symptom duration (days): 52
tmz during rt: Yes
tmz post rt: Yes
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 0.048336 AA 0.794377 11.887261
AFFX-2315061 AA 0.020644 AA 0.896327 10.805550
AFFX-2315062 AB 0.003264 AB -0.180271 9.958663
AFFX-2315057 AB 0.009826 AB -0.186887 10.137725
AFFX-2315058 AA 0.078838 AA 0.830657 11.179622
AFFX-2315059 AA 0.078713 AA 0.859971 10.042801
AFFX-2315063 AB 0.004280 AB -0.164250 10.477183
AFFX-2315064 AA 0.005206 AA 0.852220 10.197555
AFFX-2315065 BB 0.066864 BB -0.650469 9.626513
AFFX-2315066 BB 0.026243 BB -0.788905 10.074223
AFFX-2315067 AB 0.003219 AB 0.088342 10.728648
AFFX-2315068 AA 0.052254 AA 0.869595 10.490035
AFFX-2315069 AB 0.003095 AB -0.085626 10.205574
AFFX-2315070 AB 0.425349 AB 0.429827 9.889873
AFFX-2315071 BB 0.091807 BB -0.757436 9.551208
AFFX-2315072 AA 0.035941 AA 0.738700 10.514139
AFFX-2315073 AB 0.050855 AB -0.081133 10.010020
AFFX-2315074 BB 0.072481 BB -0.709818 9.359369
AFFX-2315075 AB 0.006116 AB 0.061365 10.966434
AFFX-2315076 BB 0.048339 BB -0.675916 10.043602

Total number of rows: 262314

Table truncated, full table size 12293 Kbytes.

Supplementary file Size Download File type/resource
GSM466775.CEL.gz 24.7 Mb (ftp)(http) CEL
GSM466775.CHP.gz 4.3 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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