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Sample GSM917624 Query DataSets for GSM917624
Status Public on Jul 27, 2012
Title Primary medulloblastoma sample_MDT-MB-154 [SNP]
Sample type genomic
 
Source name Primary medulloblastoma
Organism Homo sapiens
Characteristics cell type: Primary medulloblastoma
age: 8.0
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-154
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 0.003275 BB 704.646057 2227.576416
SNP_A-1967418 AB 0.045014 AB 738.634888 1002.107788
SNP_A-1969580 BB 0.027868 BB 2453.513428 6982.154297
SNP_A-4263484 AB 0.002663 AB 1650.323975 986.978577
SNP_A-1978185 AA 0.003774 AA 1394.073242 273.333954
SNP_A-4264431 AA 0.006294 AA 3170.313477 438.787781
SNP_A-1980898 AB 0.009180 AB 1088.344360 1223.552490
SNP_A-1983139 AA 0.004682 AA 1646.170410 579.934265
SNP_A-4265735 AA 0.001041 AA 1600.101807 366.722748
SNP_A-1995832 AB 0.000734 AB 1399.739990 1195.654663
SNP_A-1995893 AB 0.018246 AB 1897.582642 1483.335938
SNP_A-1997689 BB 0.000597 BB 676.413818 3127.170166
SNP_A-1997709 AA 0.002677 AA 1557.195068 240.021332
SNP_A-1997896 AA 0.005309 AA 1851.708740 573.110291
SNP_A-1997922 AB 0.025685 AB 1085.552734 581.064819
SNP_A-2000230 AA 0.000757 AA 2499.566406 969.808105
SNP_A-2000332 AB 0.006116 AB 2054.131592 2562.365234
SNP_A-2000337 AA 0.005220 AA 1917.831055 285.135651
SNP_A-2000342 AA 0.014116 AA 3255.255127 1176.229370
SNP_A-4268172 AB 0.023965 AB 649.612244 1185.069214

Total number of rows: 934968

Table truncated, full table size 47495 Kbytes.




Supplementary file Size Download File type/resource
GSM917624_MT340_MDT-MB-154.CEL.gz 29.8 Mb (ftp)(http) CEL
GSM917624_MT340_MDT-MB-154.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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