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Sample GSM466784 Query DataSets for GSM466784
Status Public on Jun 08, 2010
Title Diffuse Intrinsic Pontine Glioma 3 - Normal-250knsp
Sample type genomic
 
Source name Diffuse Intrinsic Pontine Glioma 3 - Normal
Organism Homo sapiens
Characteristics cell type: normal brain
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_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
E-mail(s) pawel.buczkowicz@sickkids.ca
Organization name Hospital for Sick Children
Department Paediatric Laboratory Medicine
Lab BTRC
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
ID_REF PROBE SET NAME
VALUE CALL
CONFIDENCE
FORCED CALL
CONTRAST
STRENGTH

Data table
ID_REF VALUE CONFIDENCE FORCED CALL CONTRAST STRENGTH
AFFX-2315060 AB 0.000295 AB -0.018914 11.744065
AFFX-2315061 AA 0.055718 AA 0.840195 10.422854
AFFX-2315062 AA 0.000516 AA 0.596029 9.907682
AFFX-2315057 AB 0.007966 AB -0.122770 10.227173
AFFX-2315058 AB 0.228445 AB 0.509294 11.122572
AFFX-2315059 BB 0.001944 BB -0.695327 9.785212
AFFX-2315063 AA 0.004993 AA 0.851069 10.047554
AFFX-2315064 AB 0.022889 AB -0.076155 10.151203
AFFX-2315065 AA 0.019383 AA 0.620904 9.436069
AFFX-2315066 AA 0.006329 AA 0.766047 9.836392
AFFX-2315067 BB 0.068421 BB -0.587857 10.487422
AFFX-2315068 BB 0.014235 BB -0.708746 9.885093
AFFX-2315069 AA 0.005433 AA 0.781354 9.841631
AFFX-2315070 AB 0.002196 AB -0.185221 10.337517
AFFX-2315071 AA 0.031520 AA 0.808784 9.349681
AFFX-2315072 AB 0.000156 AB 0.045520 10.394905
AFFX-2315073 AA 0.011658 AA 0.785067 10.311519
AFFX-2315074 AB 0.039301 AB -0.229043 9.446583
AFFX-2315075 AB 0.082378 AB 0.367295 10.890156
AFFX-2315076 BB 0.152164 BB -0.456378 9.765867

Total number of rows: 262314

Table truncated, full table size 12290 Kbytes.




Supplementary file Size Download File type/resource
GSM466784.CEL.gz 25.7 Mb (ftp)(http) CEL
GSM466784.CHP.gz 4.3 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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