GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM466772 Query DataSets for GSM466772
Status Public on Jun 08, 2010
Title Diffuse Intrinsic Pontine Glioma 1 - Tumour-250knsp
Sample type genomic
Source name Diffuse Intrinsic Pontine Glioma 1 - Tumour
Organism Homo sapiens
Characteristics cell type: DIPG*
gender: F
age at dx (years): 5.1
os (months): 4.1
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 0.023831 AA 0.705997 11.797825
AFFX-2315061 AB 0.020643 AB -0.124630 10.552706
AFFX-2315062 AA 0.027149 AA 0.645132 9.862453
AFFX-2315057 BB 0.002914 BB -0.745551 10.466581
AFFX-2315058 AB 0.001299 AB 0.221382 10.779890
AFFX-2315059 AB 0.002797 AB 0.255590 9.943156
AFFX-2315063 AB 0.003481 AB -0.159293 10.462339
AFFX-2315064 BB 0.001718 BB -0.779567 10.018980
AFFX-2315065 AB 0.008101 AB -0.192806 9.841312
AFFX-2315066 AA 0.000179 AA 0.735468 9.699961
AFFX-2315067 BB 0.009663 BB -0.588933 10.723374
AFFX-2315068 BB 0.077089 BB -0.647387 10.140865
AFFX-2315069 AB 0.003960 AB -0.037170 9.999602
AFFX-2315070 AB 0.040599 AB -0.369886 10.170300
AFFX-2315071 AB 0.047243 AB 0.227281 9.210444
AFFX-2315072 BB 0.039854 BB -0.790428 10.594633
AFFX-2315073 BB 0.011094 BB -0.642838 10.090107
AFFX-2315074 AB 0.003433 AB -0.114902 9.836716
AFFX-2315075 NC 0.911537 BB -0.376111 10.759727
AFFX-2315076 AB 0.016130 AB -0.040340 10.381218

Total number of rows: 262314

Table truncated, full table size 12287 Kbytes.

Supplementary file Size Download File type/resource
GSM466772.CEL.gz 25.2 Mb (ftp)(http) CEL
GSM466772.CHP.gz 4.3 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap