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Sample GSM917712 Query DataSets for GSM917712
Status Public on Jul 27, 2012
Title Primary medulloblastoma sample_MDT-MB-305 [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: Group 4
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-305
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 AB 0.005191 AB 1173.833740 1279.292358
SNP_A-1967418 BB 0.001343 BB 272.077179 833.713928
SNP_A-1969580 BB 0.016916 BB 2210.247070 6514.104492
SNP_A-4263484 AB 0.001991 AB 1839.252686 1281.461792
SNP_A-1978185 AA 0.001962 AA 1092.463257 287.777618
SNP_A-4264431 AA 0.009868 AA 3267.745117 383.540955
SNP_A-1980898 BB 0.005642 BB 379.251526 1865.031250
SNP_A-1983139 AA 0.006226 AA 1107.249268 345.655579
SNP_A-4265735 AB 0.000329 AB 1051.299316 1045.191284
SNP_A-1995832 BB 0.002663 BB 424.882385 1692.864380
SNP_A-1995893 BB 0.007669 BB 319.894226 1714.002441
SNP_A-1997689 BB 0.004225 BB 645.986328 2609.715088
SNP_A-1997709 AA 0.002314 AA 1461.784546 257.644531
SNP_A-1997896 AB 0.013093 AB 1920.074707 2774.824219
SNP_A-1997922 AB 0.001731 AB 979.708374 996.734863
SNP_A-2000230 AA 0.005981 AA 2762.958740 845.299500
SNP_A-2000332 AA 0.004000 AA 3680.863770 683.731445
SNP_A-2000337 AA 0.001615 AA 1682.157471 300.708282
SNP_A-2000342 AA 0.003090 AA 3341.675293 989.463440
SNP_A-4268172 AB 0.048852 AB 740.577271 1307.242920

Total number of rows: 934968

Table truncated, full table size 47496 Kbytes.




Supplementary file Size Download File type/resource
GSM917712_MT6_MDT-MB-305.CEL.gz 29.1 Mb (ftp)(http) CEL
GSM917712_MT6_MDT-MB-305.birdseed.chp.gz 13.5 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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