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Sample GSM466777 Query DataSets for GSM466777
Status Public on Jun 08, 2010
Title Diffuse Intrinsic Pontine Glioma 6 - Tumour-250knsp
Sample type genomic
Source name Diffuse Intrinsic Pontine Glioma 6 - Tumour
Organism Homo sapiens
Characteristics cell type: DIPG
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_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 0.023081 AB 0.088060 12.164114
AFFX-2315061 AB 0.000432 AB 0.140708 10.681786
AFFX-2315062 BB 0.079441 BB -0.737879 9.855030
AFFX-2315057 BB 0.275763 BB -0.697772 9.860994
AFFX-2315058 AA 0.008372 AA 0.760687 11.056761
AFFX-2315059 AA 0.000483 AA 0.787067 9.994722
AFFX-2315063 AA 0.024117 AA 0.876147 10.397025
AFFX-2315064 AB 0.014603 AB 0.267264 10.459478
AFFX-2315065 AA 0.001680 AA 0.574141 9.456085
AFFX-2315066 AA 0.007269 AA 0.757980 9.851585
AFFX-2315067 AA 0.013881 AA 0.605844 10.827064
AFFX-2315068 BB 0.039508 BB -0.731247 9.820200
AFFX-2315069 AA 0.127530 AA 0.666219 9.733452
AFFX-2315070 BB 0.060053 BB -0.872344 10.439977
AFFX-2315071 AB 0.025946 AB 0.168576 9.412277
AFFX-2315072 AA 0.023073 AA 0.724395 10.452226
AFFX-2315073 BB 0.043178 BB -0.724377 10.505285
AFFX-2315074 BB 0.022437 BB -0.776767 9.760365
AFFX-2315075 AA 0.011573 AA 0.746988 11.175187
AFFX-2315076 BB 0.010509 BB -0.620860 9.966262

Total number of rows: 262314

Table truncated, full table size 12293 Kbytes.

Supplementary file Size Download File type/resource
GSM466777.CEL.gz 25.0 Mb (ftp)(http) CEL
GSM466777.CHP.gz 4.3 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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