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Sample GSM917713 Query DataSets for GSM917713
Status Public on Jul 27, 2012
Title Primary medulloblastoma sample_MDT-MB-306 [SNP]
Sample type genomic
 
Source name Primary medulloblastoma
Organism Homo sapiens
Characteristics cell type: Primary medulloblastoma
age: 4.0
gender: F
histological subtype: Large Cell/Anaplastic
subgroup: Group 3
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-306
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 BB 0.023217 BB 765.634460 1892.883301
SNP_A-1967418 BB 0.003181 BB 319.742523 800.697693
SNP_A-1969580 BB 0.002026 BB 1566.609863 5136.455566
SNP_A-4263484 AB 0.002035 AB 1627.689697 1235.051758
SNP_A-1978185 AA 0.008430 AA 837.013245 279.521667
SNP_A-4264431 AB 0.000377 AB 1695.419434 1270.267456
SNP_A-1980898 AA 0.001462 AA 1807.577148 344.185547
SNP_A-1983139 AA 0.006783 AA 1074.187378 365.819427
SNP_A-4265735 AA 0.000959 AA 1718.465698 398.684479
SNP_A-1995832 BB 0.002361 BB 438.051849 1596.679199
SNP_A-1995893 BB 0.004265 BB 337.793976 1876.305786
SNP_A-1997689 BB 0.002889 BB 531.306458 2900.550537
SNP_A-1997709 AA 0.004808 AA 1440.521606 224.031128
SNP_A-1997896 AB 0.013340 AB 2006.158936 2660.057617
SNP_A-1997922 AB 0.017245 AB 1260.828613 1231.531738
SNP_A-2000230 AA 0.004004 AA 2719.274658 889.335693
SNP_A-2000332 AB 0.003934 AB 2840.754639 2646.183838
SNP_A-2000337 AA 0.002756 AA 1413.715942 263.518127
SNP_A-2000342 AA 0.002843 AA 3237.571777 956.498413
SNP_A-4268172 AB 0.009707 AB 741.761963 1172.323608

Total number of rows: 934968

Table truncated, full table size 47489 Kbytes.




Supplementary file Size Download File type/resource
GSM917713_MT7_MDT-MB-306.CEL.gz 29.1 Mb (ftp)(http) CEL
GSM917713_MT7_MDT-MB-306.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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