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Sample GSM466783 Query DataSets for GSM466783
Status Public on Jun 08, 2010
Title Diffuse Intrinsic Pontine Glioma 1 - Normal-250knsp
Sample type genomic
Source name Diffuse Intrinsic Pontine Glioma 1 - Normal
Organism Homo sapiens
Characteristics cell type: normal brain
gender: F
age at dx (years): 5.1
os (months): 5.1
symptoms: LTS, CN
symptom duration (days): 1
tmz during rt: No
tmz post rt: No
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 0.033264 AA 0.748666 11.554745
AFFX-2315061 AB 0.011937 AB 0.272328 10.843264
AFFX-2315062 AA 0.007579 AA 0.618104 9.891098
AFFX-2315057 BB 0.017809 BB -0.732876 10.286936
AFFX-2315058 AB 0.010374 AB 0.312218 10.835710
AFFX-2315059 AB 0.000381 AB 0.199794 9.968781
AFFX-2315063 AB 0.011184 AB -0.171233 10.104094
AFFX-2315064 BB 0.008926 BB -0.739352 9.851796
AFFX-2315065 AB 0.016552 AB -0.049869 9.510246
AFFX-2315066 AA 0.035603 AA 0.822702 9.946620
AFFX-2315067 BB 0.047315 BB -0.635358 10.782452
AFFX-2315068 BB 0.008660 BB -0.727108 10.178709
AFFX-2315069 AB 0.000574 AB -0.160955 10.142136
AFFX-2315070 AB 0.008603 AB -0.063404 9.967330
AFFX-2315071 AB 0.004878 AB -0.146901 9.466368
AFFX-2315072 BB 0.002116 BB -0.774610 10.370192
AFFX-2315073 BB 0.003736 BB -0.696953 10.272947
AFFX-2315074 AB 0.004985 AB -0.106853 9.557740
AFFX-2315075 AB 0.004026 AB 0.173039 10.906594
AFFX-2315076 AB 0.001100 AB 0.015642 10.007490

Total number of rows: 262314

Table truncated, full table size 12293 Kbytes.

Supplementary file Size Download File type/resource
GSM466783.CEL.gz 25.6 Mb (ftp)(http) CEL
GSM466783.CHP.gz 4.3 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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