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Sample GSM466774 Query DataSets for GSM466774
Status Public on Jun 08, 2010
Title Diffuse Intrinsic Pontine Glioma 3 - Tumour-250knsp
Sample type genomic
Source name Diffuse Intrinsic Pontine Glioma 3 - Tumour
Organism Homo sapiens
Characteristics cell type: DIPG
gender: M
age at dx (years): 5.14
os (months): 11.51
symptoms: LTS, ataxia, CN
symptom duration (days): ≤180
tmz during rt: No
tmz post rt: No
other chemo: Nimotuzumab2
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 0.019030 AB -0.169362 11.734531
AFFX-2315061 AA 0.025851 AA 0.893213 10.896968
AFFX-2315062 AA 0.027487 AA 0.661970 10.006067
AFFX-2315057 AB 0.384155 AB -0.464982 9.921510
AFFX-2315058 AB 0.031019 AB 0.325673 11.165666
AFFX-2315059 BB 0.027431 BB -0.784545 10.034768
AFFX-2315063 AA 0.033498 AA 0.854151 9.850388
AFFX-2315064 AB 0.068829 AB 0.435858 10.174233
AFFX-2315065 AA 0.025719 AA 0.616808 9.378812
AFFX-2315066 AA 0.056158 AA 0.685919 9.365551
AFFX-2315067 BB 0.048962 BB -0.621575 10.936034
AFFX-2315068 BB 0.006752 BB -0.740446 10.167315
AFFX-2315069 AA 0.013180 AA 0.825350 9.967603
AFFX-2315070 AB 0.029351 AB 0.155333 10.247305
AFFX-2315071 AA 0.015234 AA 0.786346 9.065871
AFFX-2315072 AB 0.040917 AB 0.278013 10.489417
AFFX-2315073 AA 0.030043 AA 0.806657 10.318807
AFFX-2315074 AA 0.133824 AA 0.635494 8.934414
AFFX-2315075 AB 0.046541 AB -0.023639 10.688810
AFFX-2315076 AB 0.109913 AB 0.174376 9.607309

Total number of rows: 262314

Table truncated, full table size 12290 Kbytes.

Supplementary file Size Download File type/resource
GSM466774.CEL.gz 25.1 Mb (ftp)(http) CEL
GSM466774.CHP.gz 4.3 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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