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Sample GSM466786 Query DataSets for GSM466786
Status Public on Jun 08, 2010
Title Diffuse Intrinsic Pontine Glioma 6 - Normal-250knsp
Sample type genomic
Source name Diffuse Intrinsic Pontine Glioma 6 - Normal
Organism Homo sapiens
Characteristics cell type: normal brain
gender: M
age at dx (years): 7.17
os (months): 6
symptoms: Ataxia, CN
symptom duration (days): 60
tmz during rt: No
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_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 AB 0.002358 AB -0.058183 11.784848
AFFX-2315061 AB 0.001766 AB 0.042275 10.789915
AFFX-2315062 BB 0.085191 BB -0.648550 10.142415
AFFX-2315057 BB 0.028655 BB -0.694646 10.366338
AFFX-2315058 AA 0.072576 AA 0.743922 11.191814
AFFX-2315059 AA 0.231015 AA 0.702902 10.062416
AFFX-2315063 AA 0.011856 AA 0.800477 9.899632
AFFX-2315064 AB 0.000888 AB 0.236297 10.174994
AFFX-2315065 AA 0.037229 AA 0.520879 9.500729
AFFX-2315066 AA 0.022226 AA 0.754792 9.935827
AFFX-2315067 AA 0.014974 AA 0.603160 10.934744
AFFX-2315068 BB 0.028045 BB -0.678431 10.129415
AFFX-2315069 AB 0.020366 AB -0.338553 10.190522
AFFX-2315070 BB 0.007946 BB -0.831521 10.257693
AFFX-2315071 AB 0.004009 AB -0.190587 9.238011
AFFX-2315072 AA 0.021312 AA 0.716862 10.534862
AFFX-2315073 BB 0.001872 BB -0.689034 10.136383
AFFX-2315074 BB 0.005470 BB -0.738644 9.632133
AFFX-2315075 AA 0.002194 AA 0.712444 11.017551
AFFX-2315076 BB 0.007479 BB -0.616402 10.036545

Total number of rows: 262314

Table truncated, full table size 12292 Kbytes.

Supplementary file Size Download File type/resource
GSM466786.CEL.gz 25.5 Mb (ftp)(http) CEL
GSM466786.CHP.gz 4.3 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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