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Sample GSM466776 Query DataSets for GSM466776
Status Public on Jun 08, 2010
Title Diffuse Intrinsic Pontine Glioma 5 - Tumour-250knsp
Sample type genomic
 
Source name Diffuse Intrinsic Pontine Glioma 5 - Tumour
Organism Homo sapiens
Characteristics cell type: DIPG
gender: F
age at dx (years): 8.96
os (months): 11.64
symptoms: Ataxia, CN
symptom duration (days): 60
tmz during rt: Yes
tmz post rt: Yes
other chemo: Tipifarnib2
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
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 0.000170 AB 0.004703 11.674302
AFFX-2315061 AB 0.324974 AB 0.508382 10.427368
AFFX-2315062 AB 0.045757 AB -0.275887 9.852563
AFFX-2315057 BB 0.027868 BB -0.781882 10.555403
AFFX-2315058 AA 0.064001 AA 0.801020 11.273964
AFFX-2315059 AB 0.003153 AB 0.263192 9.954881
AFFX-2315063 AB 0.004890 AB -0.128789 10.534420
AFFX-2315064 AA 0.029115 AA 0.895249 10.459538
AFFX-2315065 AB 0.005385 AB -0.223817 9.728327
AFFX-2315066 BB 0.002925 BB -0.716641 9.865690
AFFX-2315067 BB 0.088234 BB -0.656432 10.691784
AFFX-2315068 BB 0.009747 BB -0.758343 10.118432
AFFX-2315069 AB 0.000359 AB -0.130139 10.041002
AFFX-2315070 AA 0.012450 AA 0.840270 10.033495
AFFX-2315071 AB 0.001173 AB -0.148136 9.246930
AFFX-2315072 AA 0.011013 AA 0.658464 10.304543
AFFX-2315073 BB 0.015182 BB -0.733650 10.209883
AFFX-2315074 BB 0.080126 BB -0.747264 9.424109
AFFX-2315075 AA 0.060175 AA 0.805957 11.206795
AFFX-2315076 BB 0.067202 BB -0.704590 10.212211

Total number of rows: 262314

Table truncated, full table size 12297 Kbytes.




Supplementary file Size Download File type/resource
GSM466776.CEL.gz 25.6 Mb (ftp)(http) CEL
GSM466776.CHP.gz 4.3 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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