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Sample GSM917692 Query DataSets for GSM917692
Status Public on Jul 27, 2012
Title Primary medulloblastoma sample_MDT-MB-212 [SNP]
Sample type genomic
 
Source name Primary medulloblastoma
Organism Homo sapiens
Characteristics cell type: Primary medulloblastoma
age: 10.0
gender: F
histological subtype: Classic
subgroup: N/A
Treatment protocol N/A
Growth protocol N/A
Extracted molecule genomic DNA
Extraction protocol High molecular weight genomic DNA was extracted from primary tissue and cell lines using either the standard SDS/Proteinase K method or Qiagen DNEasy Blood and Tissue Kits.
Label Biotin
Label protocol As directed by the manufacturer (Affymetrix)
 
Hybridization protocol As directed by the manufacturer (Affymetrix)
Scan protocol As directed by the manufacturer (Affymetrix)
Description MDT-MB-212
Data processing SNP genotyping was performed using the birdseed algorithm (v2) available in Affymetrix Genotyping Console 4.0. For copy number analysis, CEL files were quantile normalized and signal intensities estimated using the MBEI method in dChip.
 
Submission date Apr 18, 2012
Last update date Jul 27, 2012
Contact name Paul A. Northcott
E-mail(s) panorthcott@gmail.com
Organization name German Cancer Research Center (DKFZ)
Street address Im Neuenheimer Feld 280
City HEIDELBERG
ZIP/Postal code 69120
Country Germany
 
Platform ID GPL6801
Series (2)
GSE37384 Subgroup specific somatic copy number aberrations in the medulloblastoma genome [gDNA]
GSE37385 Subgroup specific somatic copy number aberrations in the medulloblastoma genome

Data table header descriptions
ID_REF PROBE SET NAME
VALUE CALL
CONFIDENCE
FORCED CALL
SIGNAL A
SIGNAL B

Data table
ID_REF VALUE CONFIDENCE FORCED CALL SIGNAL A SIGNAL B
SNP_A-2131660 AA 0.001278 AA 2229.212402 543.249756
SNP_A-1967418 AB 0.005750 AB 718.742615 643.193542
SNP_A-1969580 BB 0.017119 BB 1380.289062 5762.461426
SNP_A-4263484 AB 0.001533 AB 1741.782104 1089.634399
SNP_A-1978185 AA 0.006965 AA 873.003296 257.912201
SNP_A-4264431 AA 0.012897 AA 3234.812988 319.253754
SNP_A-1980898 BB 0.004574 BB 282.240814 1734.292725
SNP_A-1983139 AA 0.008763 AA 2156.295410 470.327057
SNP_A-4265735 AB 0.000217 AB 1092.234253 1086.985596
SNP_A-1995832 BB 0.003763 BB 451.469391 1898.769775
SNP_A-1995893 BB 0.002824 BB 530.327576 2338.381348
SNP_A-1997689 BB 0.001297 BB 676.771301 2987.364014
SNP_A-1997709 AA 0.028869 AA 1462.118286 380.857788
SNP_A-1997896 AA 0.009457 AA 2727.203369 516.247742
SNP_A-1997922 BB 0.002308 BB 597.608643 1554.881104
SNP_A-2000230 AA 0.006838 AA 2557.384521 764.271545
SNP_A-2000332 AB 0.030230 AB 3513.765625 3273.492432
SNP_A-2000337 AA 0.002402 AA 1668.101929 253.429291
SNP_A-2000342 AA 0.008567 AA 3934.017090 794.691345
SNP_A-4268172 AA 0.001001 AA 799.983215 264.756470

Total number of rows: 934968

Table truncated, full table size 47481 Kbytes.




Supplementary file Size Download File type/resource
GSM917692_MT403_MDT-MB-212.CEL.gz 28.8 Mb (ftp)(http) CEL
GSM917692_MT403_MDT-MB-212.birdseed.chp.gz 13.4 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file
Processed data are available on Series record

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